diff --git a/Apollo.xcodeproj/project.pbxproj b/Apollo.xcodeproj/project.pbxproj
index 783a723782..eb68289c3c 100644
--- a/Apollo.xcodeproj/project.pbxproj
+++ b/Apollo.xcodeproj/project.pbxproj
@@ -14,6 +14,7 @@
 		54DDB0921EA045870009DD99 /* InMemoryNormalizedCache.swift in Sources */ = {isa = PBXBuildFile; fileRef = 54DDB0911EA045870009DD99 /* InMemoryNormalizedCache.swift */; };
 		5AC6CA4322AAF7B200B7C94D /* GraphQLHTTPMethod.swift in Sources */ = {isa = PBXBuildFile; fileRef = 5AC6CA4222AAF7B200B7C94D /* GraphQLHTTPMethod.swift */; };
 		5BB2C0232380836100774170 /* VersionNumberTests.swift in Sources */ = {isa = PBXBuildFile; fileRef = 5BB2C0222380836100774170 /* VersionNumberTests.swift */; };
+		6608B3362A7D402B006FB655 /* ApolloCodegenConfiguration+OperationManifestConfiguration.swift in Sources */ = {isa = PBXBuildFile; fileRef = 6608B3342A7D3FF5006FB655 /* ApolloCodegenConfiguration+OperationManifestConfiguration.swift */; };
 		662EA65E2A701483008A1931 /* GenerateOperationManifest.swift in Sources */ = {isa = PBXBuildFile; fileRef = 662EA65D2A701483008A1931 /* GenerateOperationManifest.swift */; };
 		662EA6602A705BD7008A1931 /* GenerateOperationManifestTests.swift in Sources */ = {isa = PBXBuildFile; fileRef = 662EA65F2A705BD7008A1931 /* GenerateOperationManifestTests.swift */; };
 		66321AE72A126C4400CC35CB /* IR+Formatting.swift in Sources */ = {isa = PBXBuildFile; fileRef = 66321AE62A126C4400CC35CB /* IR+Formatting.swift */; };
@@ -1140,6 +1141,7 @@
 		54DDB0911EA045870009DD99 /* InMemoryNormalizedCache.swift */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.swift; path = InMemoryNormalizedCache.swift; sourceTree = "<group>"; };
 		5AC6CA4222AAF7B200B7C94D /* GraphQLHTTPMethod.swift */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.swift; path = GraphQLHTTPMethod.swift; sourceTree = "<group>"; };
 		5BB2C0222380836100774170 /* VersionNumberTests.swift */ = {isa = PBXFileReference; lastKnownFileType = sourcecode.swift; path = VersionNumberTests.swift; sourceTree = "<group>"; };
+		6608B3342A7D3FF5006FB655 /* ApolloCodegenConfiguration+OperationManifestConfiguration.swift */ = {isa = PBXFileReference; lastKnownFileType = sourcecode.swift; path = "ApolloCodegenConfiguration+OperationManifestConfiguration.swift"; sourceTree = "<group>"; };
 		662EA65D2A701483008A1931 /* GenerateOperationManifest.swift */ = {isa = PBXFileReference; lastKnownFileType = sourcecode.swift; path = GenerateOperationManifest.swift; sourceTree = "<group>"; };
 		662EA65F2A705BD7008A1931 /* GenerateOperationManifestTests.swift */ = {isa = PBXFileReference; lastKnownFileType = sourcecode.swift; path = GenerateOperationManifestTests.swift; sourceTree = "<group>"; };
 		66321AE62A126C4400CC35CB /* IR+Formatting.swift */ = {isa = PBXFileReference; lastKnownFileType = sourcecode.swift; path = "IR+Formatting.swift"; sourceTree = "<group>"; };
@@ -2206,6 +2208,14 @@
 /* End PBXFrameworksBuildPhase section */
 
 /* Begin PBXGroup section */
+		6608B3332A7D3FCB006FB655 /* CodegenConfiguration */ = {
+			isa = PBXGroup;
+			children = (
+				6608B3342A7D3FF5006FB655 /* ApolloCodegenConfiguration+OperationManifestConfiguration.swift */,
+			);
+			path = CodegenConfiguration;
+			sourceTree = "<group>";
+		};
 		66B18E862A15366400525DFB /* Network */ = {
 			isa = PBXGroup;
 			children = (
@@ -2548,6 +2558,7 @@
 		9BD681332405F6BB000874CB /* Codegen */ = {
 			isa = PBXGroup;
 			children = (
+				6608B3332A7D3FCB006FB655 /* CodegenConfiguration */,
 				9B7B6F57233C287100F32205 /* ApolloCodegen.swift */,
 				9B7B6F58233C287100F32205 /* ApolloCodegenConfiguration.swift */,
 				E674DB40274C0A9B009BB90E /* Glob.swift */,
@@ -5053,6 +5064,7 @@
 				E6203342284F1C9600A291D1 /* MockUnionsFileGenerator.swift in Sources */,
 				DE6D07F927BC3B6D009F5F33 /* GraphQLInputField+Rendered.swift in Sources */,
 				9F1A966C258F34BB00A06EEB /* GraphQLSchema.swift in Sources */,
+				6608B3362A7D402B006FB655 /* ApolloCodegenConfiguration+OperationManifestConfiguration.swift in Sources */,
 				9BE74D3D23FB4A8E006D354F /* FileFinder.swift in Sources */,
 				E64F7EBC27A11A510059C021 /* GraphQLNamedType+SwiftName.swift in Sources */,
 				9B7B6F59233C287200F32205 /* ApolloCodegen.swift in Sources */,
diff --git a/Sources/ApolloCodegenLib/ApolloCodegen.swift b/Sources/ApolloCodegenLib/ApolloCodegen.swift
index 9d0d50ad8f..2b6cd3fa45 100644
--- a/Sources/ApolloCodegenLib/ApolloCodegen.swift
+++ b/Sources/ApolloCodegenLib/ApolloCodegen.swift
@@ -67,6 +67,22 @@ public class ApolloCodegen {
       }
     }
   }
+  
+  public struct ItemsToGenerate: OptionSet {
+    public var rawValue: Int
+    
+    public static let code = ItemsToGenerate(rawValue: 1 << 0)
+    public static let operationManifest = ItemsToGenerate(rawValue: 1 << 1)
+    public static let all: ItemsToGenerate = [
+      .code,
+      .operationManifest
+    ]
+    
+    public init(rawValue: Int) {
+      self.rawValue = rawValue
+    }
+    
+  }
 
   /// Executes the code generation engine with a specified configuration.
   ///
@@ -77,15 +93,17 @@ public class ApolloCodegen {
   ///     If `nil`, the current working directory of the executing process will be used.
   public static func build(
     with configuration: ApolloCodegenConfiguration,
-    withRootURL rootURL: URL? = nil
+    withRootURL rootURL: URL? = nil,
+    itemsToGenerate: ItemsToGenerate = [.code]
   ) throws {
-    try build(with: configuration, rootURL: rootURL)
+    try build(with: configuration, rootURL: rootURL, itemsToGenerate: itemsToGenerate)
   }
 
   internal static func build(
     with configuration: ApolloCodegenConfiguration,
     rootURL: URL? = nil,
-    fileManager: ApolloFileManager = .default
+    fileManager: ApolloFileManager = .default,
+    itemsToGenerate: ItemsToGenerate
   ) throws {
 
     let configContext = ConfigurationContext(
@@ -103,58 +121,43 @@ public class ApolloCodegen {
     try validate(configContext, with: compilationResult)
 
     let ir = IR(compilationResult: compilationResult)
+    
+    if itemsToGenerate == .operationManifest {
+      var operationIDsFileGenerator = OperationManifestFileGenerator(config: configContext)
+      
+      for operation in compilationResult.operations {
+        autoreleasepool {
+          let irOperation = ir.build(operation: operation)
+          operationIDsFileGenerator?.collectOperationIdentifier(irOperation)
+        }
+      }
+      
+      try operationIDsFileGenerator?.generate(fileManager: fileManager)
+    }
 
-    var existingGeneratedFilePaths = configuration.options.pruneGeneratedFiles ?
-    try findExistingGeneratedFilePaths(
-      config: configContext,
-      fileManager: fileManager
-    ) : []
-
-    try generateFiles(
-      compilationResult: compilationResult,
-      ir: ir,
-      config: configContext,
-      fileManager: fileManager
-    )
+    if itemsToGenerate.contains(.code) {
+      var existingGeneratedFilePaths = configuration.options.pruneGeneratedFiles ?
+      try findExistingGeneratedFilePaths(
+        config: configContext,
+        fileManager: fileManager
+      ) : []
 
-    if configuration.options.pruneGeneratedFiles {
-      try deleteExtraneousGeneratedFiles(
-        from: &existingGeneratedFilePaths,
-        afterCodeGenerationUsing: fileManager
+      try generateFiles(
+        compilationResult: compilationResult,
+        ir: ir,
+        config: configContext,
+        fileManager: fileManager,
+        itemsToGenerate: itemsToGenerate
       )
+
+      if configuration.options.pruneGeneratedFiles {
+        try deleteExtraneousGeneratedFiles(
+          from: &existingGeneratedFilePaths,
+          afterCodeGenerationUsing: fileManager
+        )
+      }
     }
   }
-  
-  public static func generateOperationManifest(
-    with configuration: ApolloCodegenConfiguration,
-    withRootURL rootURL: URL? = nil,
-    fileManager: ApolloFileManager = .default
-  ) throws {
-    let configContext = ConfigurationContext(
-      config: configuration,
-      rootURL: rootURL
-    )
-    
-    try validate(configContext)
-    
-    let compilationResult = try compileGraphQLResult(
-      configContext,
-      experimentalFeatures: configuration.experimentalFeatures
-    )
-    
-    try validate(configContext, with: compilationResult)
-    
-    let ir = IR(compilationResult: compilationResult)
-    
-    var operationIDsFileGenerator = OperationManifestFileGenerator(config: configContext)
-    
-    for operation in compilationResult.operations {
-      let irOperation = ir.build(operation: operation)
-      operationIDsFileGenerator?.collectOperationIdentifier(irOperation)
-    }
-    
-    try operationIDsFileGenerator?.generate(fileManager: fileManager)
-  }
 
   // MARK: Internal
 
@@ -411,7 +414,8 @@ public class ApolloCodegen {
     compilationResult: CompilationResult,
     ir: IR,
     config: ConfigurationContext,
-    fileManager: ApolloFileManager = .default
+    fileManager: ApolloFileManager = .default,
+    itemsToGenerate: ItemsToGenerate
   ) throws {
     for fragment in compilationResult.fragments {
       try autoreleasepool {
@@ -431,11 +435,15 @@ public class ApolloCodegen {
         try OperationFileGenerator(irOperation: irOperation, config: config)
           .generate(forConfig: config, fileManager: fileManager)
 
-        operationIDsFileGenerator?.collectOperationIdentifier(irOperation)
+        if itemsToGenerate.contains(.operationManifest) {
+          operationIDsFileGenerator?.collectOperationIdentifier(irOperation)
+        }
       }
     }
 
-    try operationIDsFileGenerator?.generate(fileManager: fileManager)
+    if itemsToGenerate.contains(.operationManifest) {
+      try operationIDsFileGenerator?.generate(fileManager: fileManager)
+    }
     operationIDsFileGenerator = nil
 
     for graphQLObject in ir.schema.referencedTypes.objects {
diff --git a/Sources/ApolloCodegenLib/ApolloCodegenConfiguration.swift b/Sources/ApolloCodegenLib/ApolloCodegenConfiguration.swift
index 63b5348a8d..974b8a0b59 100644
--- a/Sources/ApolloCodegenLib/ApolloCodegenConfiguration.swift
+++ b/Sources/ApolloCodegenLib/ApolloCodegenConfiguration.swift
@@ -164,16 +164,15 @@ public struct ApolloCodegenConfiguration: Codable, Equatable {
     public let operations: OperationsFileOutput
     /// The local path structure for the test mock operation object files.
     public let testMocks: TestMockFileOutput
-    /// Configures the generation of an operation manifest JSON file for use with persisted queries
-    /// or [Automatic Persisted Queries (APQs)](https://www.apollographql.com/docs/apollo-server/performance/apq).
-    /// Defaults to `nil`.
-    public let operationManifest: OperationManifestFileOutput?
+    
+    /// This var helps maintain backwards compatibility with legacy operation manifest generation
+    /// with the new `OperationManifestConfiguration` and will be fully removed in v2.0
+    fileprivate let operationIDsPath: String?
 
     /// Default property values
     public struct Default {
       public static let operations: OperationsFileOutput = .inSchemaModule
       public static let testMocks: TestMockFileOutput = .none
-      public static let operationManifest: OperationManifestFileOutput? = nil
     }
 
     /// Designated initializer.
@@ -191,13 +190,12 @@ public struct ApolloCodegenConfiguration: Codable, Equatable {
     public init(
       schemaTypes: SchemaTypesFileOutput,
       operations: OperationsFileOutput = Default.operations,
-      testMocks: TestMockFileOutput = Default.testMocks,
-      operationManifest: OperationManifestFileOutput? = Default.operationManifest
+      testMocks: TestMockFileOutput = Default.testMocks
     ) {
       self.schemaTypes = schemaTypes
       self.operations = operations
       self.testMocks = testMocks
-      self.operationManifest = operationManifest
+      self.operationIDsPath = nil
     }
 
     // MARK: Codable
@@ -206,7 +204,6 @@ public struct ApolloCodegenConfiguration: Codable, Equatable {
       case schemaTypes
       case operations
       case testMocks
-      case operationManifest
       case operationIdentifiersPath
     }
 
@@ -228,21 +225,10 @@ public struct ApolloCodegenConfiguration: Codable, Equatable {
         forKey: .testMocks
       )
 
-      if let operationManifest = try values.decodeIfPresent(
-        OperationManifestFileOutput.self,
-        forKey: .operationManifest
-      ) {
-        self.operationManifest = operationManifest
-
-      } else if let operationIdsPath = try values.decodeIfPresent(
+      operationIDsPath = try values.decodeIfPresent(
         String.self,
         forKey: .operationIdentifiersPath
-      ){
-        self.operationManifest = .init(path: operationIdsPath, version: .legacyAPQ)
-
-      } else {
-        self.operationManifest = nil
-      }
+      )
     }
 
     public func encode(to encoder: Encoder) throws {
@@ -251,7 +237,6 @@ public struct ApolloCodegenConfiguration: Codable, Equatable {
       try container.encode(self.schemaTypes, forKey: .schemaTypes)
       try container.encode(self.operations, forKey: .operations)
       try container.encode(self.testMocks, forKey: .testMocks)
-      try container.encode(self.operationManifest, forKey: .operationManifest)
     }
   }
 
@@ -470,41 +455,6 @@ public struct ApolloCodegenConfiguration: Codable, Equatable {
     }
   }
 
-  /// Configures the generation of an operation manifest JSON file for use with persisted queries
-  /// or [Automatic Persisted Queries (APQs)](https://www.apollographql.com/docs/apollo-server/performance/apq).
-  ///
-  /// The operation manifest is a JSON file that maps all generated GraphQL operations to an
-  /// operation identifier. This manifest can be used to register operations with a server utilizing
-  /// persisted queries
-  /// or [Automatic Persisted Queries (APQs)](https://www.apollographql.com/docs/apollo-server/performance/apq).
-  /// Defaults to `nil`.
-  public struct OperationManifestFileOutput: Codable, Equatable {
-    /// Local path where the generated operation manifest file should be written.
-    let path: String
-    /// The version format to use when generating the operation manifest. Defaults to `.persistedQueries`.
-    let version: Version
-
-    public enum Version: String, Codable, Equatable {
-      /// Generates an operation manifest for use with persisted queries.
-      case persistedQueries
-      /// Generates an operation manifest for pre-registering operations with the legacy
-      /// [Automatic Persisted Queries (APQs)](https://www.apollographql.com/docs/apollo-server/performance/apq).
-      /// functionality of Apollo Server/Router.
-      case legacyAPQ
-    }
-
-    /// Designated Initializer
-    /// - Parameters:
-    ///   - path: Local path where the generated operation manifest file should be written.
-    ///   - version: The version format to use when generating the operation manifest.
-    ///   Defaults to `.persistedQueries`.
-    public init(path: String, version: Version = .persistedQueries) {
-      self.path = path
-      self.version = version
-    }
-
-  }
-
   // MARK: - Other Types
   public struct OutputOptions: Codable, Equatable {
     /// Any non-default rules for pluralization or singularization you wish to include.
@@ -750,7 +700,9 @@ public struct ApolloCodegenConfiguration: Codable, Equatable {
       ) ?? Default.enumCases
     }
   }
-
+  
+  // MARK: - OperationDocumentFormat
+  
   public struct OperationDocumentFormat: OptionSet, Codable, Equatable {
     /// Include the GraphQL source document for the operation in the generated operation models.
     public static let definition = Self(rawValue: 1)
@@ -944,7 +896,7 @@ public struct ApolloCodegenConfiguration: Codable, Equatable {
   /// The input files required for code generation.
   public let input: FileInput
   /// The paths and files output by code generation.
-  public let output: FileOutput
+  public var output: FileOutput
   /// Rules and options to customize the generated code.
   public let options: OutputOptions
   /// Allows users to enable experimental features.
@@ -953,12 +905,15 @@ public struct ApolloCodegenConfiguration: Codable, Equatable {
   /// available.
   public let experimentalFeatures: ExperimentalFeatures
   /// Schema download configuration.
-  public let schemaDownloadConfiguration: ApolloSchemaDownloadConfiguration?
+  public let schemaDownload: ApolloSchemaDownloadConfiguration?
+  /// Configuration for generating an operation manifest for use with persisted queries.
+  public let operationManifest: OperationManifestConfiguration?
 
   public struct Default {
     public static let options: OutputOptions = OutputOptions()
     public static let experimentalFeatures: ExperimentalFeatures = ExperimentalFeatures()
-    public static let schemaDownloadConfiguration: ApolloSchemaDownloadConfiguration? = nil
+    public static let schemaDownload: ApolloSchemaDownloadConfiguration? = nil
+    public static let operationManifest: OperationManifestConfiguration? = nil
   }
 
   // MARK: - Helper Properties
@@ -981,14 +936,16 @@ public struct ApolloCodegenConfiguration: Codable, Equatable {
     output: FileOutput,
     options: OutputOptions = Default.options,
     experimentalFeatures: ExperimentalFeatures = Default.experimentalFeatures,
-    schemaDownloadConfiguration: ApolloSchemaDownloadConfiguration? = Default.schemaDownloadConfiguration
+    schemaDownload: ApolloSchemaDownloadConfiguration? = Default.schemaDownload,
+    operationManifest: OperationManifestConfiguration? = Default.operationManifest
   ) {
     self.schemaNamespace = schemaNamespace
     self.input = input
     self.output = output
     self.options = options
     self.experimentalFeatures = experimentalFeatures
-    self.schemaDownloadConfiguration = schemaDownloadConfiguration
+    self.schemaDownload = schemaDownload
+    self.operationManifest = operationManifest
     self.ApolloAPITargetName = options.cocoapodsCompatibleImportStatements ? "Apollo" : "ApolloAPI"
   }
 
@@ -1002,6 +959,8 @@ public struct ApolloCodegenConfiguration: Codable, Equatable {
     case options
     case experimentalFeatures
     case schemaDownloadConfiguration
+    case schemaDownload
+    case operationManifest
   }
 
   public func encode(to encoder: Encoder) throws {
@@ -1013,8 +972,12 @@ public struct ApolloCodegenConfiguration: Codable, Equatable {
     try container.encode(self.options, forKey: .options)
     try container.encode(experimentalFeatures, forKey: .experimentalFeatures)
 
-    if let schemaDownloadConfiguration {
-      try container.encode(schemaDownloadConfiguration, forKey: .schemaDownloadConfiguration)
+    if let schemaDownload {
+      try container.encode(schemaDownload, forKey: .schemaDownload)
+    }
+    
+    if let operationManifest {
+      try container.encode(operationManifest, forKey: .operationManifest)
     }
   }
 
@@ -1038,23 +1001,39 @@ public struct ApolloCodegenConfiguration: Codable, Equatable {
         )
       )
     }
+    
+    let fileOutput = try values.decode(FileOutput.self, forKey: .output)
+    let options = try values.decodeIfPresent(
+      OutputOptions.self,
+      forKey: .options
+    ) ?? Default.options
+    
+    var operationManifest = try values.decodeIfPresent(OperationManifestConfiguration.self, forKey: .operationManifest)
+    if operationManifest == nil {
+      if let operationIDsPath = fileOutput.operationIDsPath {
+        operationManifest = OperationManifestConfiguration(
+          path: operationIDsPath,
+          version: .legacy
+        )
+      }
+    }
+    
+    var schemaDownload = try values.decodeIfPresent(ApolloSchemaDownloadConfiguration.self, forKey: .schemaDownload)
+    if schemaDownload == nil {
+      schemaDownload = try values.decodeIfPresent(ApolloSchemaDownloadConfiguration.self, forKey: .schemaDownloadConfiguration)
+    }
 
     self.init(
       schemaNamespace: try getSchemaNamespaceValue(),
       input: try values.decode(FileInput.self, forKey: .input),
-      output: try values.decode(FileOutput.self, forKey: .output),
-      options: try values.decodeIfPresent(
-        OutputOptions.self,
-        forKey: .options
-      ) ?? Default.options,
+      output: fileOutput,
+      options: options,
       experimentalFeatures: try values.decodeIfPresent(
         ExperimentalFeatures.self,
         forKey: .experimentalFeatures
       ) ?? Default.experimentalFeatures,
-      schemaDownloadConfiguration: try values.decodeIfPresent(
-        ApolloSchemaDownloadConfiguration.self,
-        forKey: .schemaDownloadConfiguration
-      ) ?? Default.schemaDownloadConfiguration
+      schemaDownload: schemaDownload ?? Default.schemaDownload,
+      operationManifest: operationManifest ?? Default.operationManifest
     )
   }
 }
@@ -1193,7 +1172,7 @@ extension ApolloCodegenConfiguration {
   @available(*, deprecated, renamed: "schemaNamespace")
   public var schemaName: String { schemaNamespace }
 
-  /// Deprecated initializer - use `init(schemaNamespace:input:output:options:experimentalFeatures:schemaDownloadConfiguration:)`
+  /// Deprecated initializer - use `init(schemaNamespace:input:output:options:experimentalFeatures:schemaDownload:operationManifest:)`
   /// instead.
   ///
   /// - Parameters:
@@ -1202,14 +1181,14 @@ extension ApolloCodegenConfiguration {
   ///  - output: The paths and files output by code generation.
   ///  - options: Rules and options to customize the generated code.
   ///  - experimentalFeatures: Allows users to enable experimental features.
-  @available(*, deprecated, renamed: "init(schemaNamespace:input:output:options:experimentalFeatures:schemaDownloadConfiguration:)")
+  @available(*, deprecated, renamed: "init(schemaNamespace:input:output:options:experimentalFeatures:schemaDownload:operationManifest:)")
   public init(
     schemaName: String,
     input: FileInput,
     output: FileOutput,
     options: OutputOptions = Default.options,
     experimentalFeatures: ExperimentalFeatures = Default.experimentalFeatures,
-    schemaDownloadConfiguration: ApolloSchemaDownloadConfiguration? = Default.schemaDownloadConfiguration
+    schemaDownloadConfiguration: ApolloSchemaDownloadConfiguration? = Default.schemaDownload
   ) {
     self.init(
       schemaNamespace: schemaName,
@@ -1217,7 +1196,7 @@ extension ApolloCodegenConfiguration {
       output: output,
       options: options,
       experimentalFeatures: experimentalFeatures,
-      schemaDownloadConfiguration: schemaDownloadConfiguration)
+      schemaDownload: schemaDownloadConfiguration)
   }
 
   /// Enum to enable using
@@ -1271,7 +1250,7 @@ extension ApolloCodegenConfiguration.FileOutput {
   ///  If `.none`, test mocks will not be generated. Defaults to `.none`.
   ///  - operationIdentifiersPath: An absolute location to an operation id JSON map file
   ///  for use with APQ registration. Defaults to `nil`.
-  @available(*, deprecated, renamed: "init(schemaTypes:operations:testMocks:operationManifest:)")
+  @available(*, deprecated, renamed: "init(schemaTypes:operations:testMocks:)")
   public init(
     schemaTypes: ApolloCodegenConfiguration.SchemaTypesFileOutput,
     operations: ApolloCodegenConfiguration.OperationsFileOutput = Default.operations,
@@ -1281,16 +1260,12 @@ extension ApolloCodegenConfiguration.FileOutput {
     self.schemaTypes = schemaTypes
     self.operations = operations
     self.testMocks = testMocks
-    if let operationIdentifiersPath {
-      self.operationManifest = .init(path: operationIdentifiersPath, version: .legacyAPQ)
-    } else {
-      self.operationManifest = nil
-    }
+    self.operationIDsPath = operationIdentifiersPath
   }
 
   /// An absolute location to an operation id JSON map file.
-  @available(*, deprecated, renamed: "operationManifest.path")
-  public var operationIdentifiersPath: String? { operationManifest?.path }
+  @available(*, deprecated, message: "Moved to ApolloCodegenConfiguration.OperationManifestConfiguration.OperationManifest.path")
+  public var operationIdentifiersPath: String? { operationIDsPath }
 }
 
 extension ApolloCodegenConfiguration.OutputOptions {
@@ -1391,17 +1366,17 @@ extension ApolloCodegenConfiguration.OutputOptions {
   /// See `APQConfig` for more information on Automatic Persisted Queries.
   @available(*, deprecated, message: "Use OperationDocumentFormat instead.")
   public var apqs: ApolloCodegenConfiguration.APQConfig {
-    switch self.operationDocumentFormat {
-    case .definition:
-      return .disabled
-    case .operationId:
-      return .persistedOperationsOnly
-    case [.operationId, .definition]:
-      return .automaticallyPersist
-    default:
-      return .disabled
+      switch self.operationDocumentFormat {
+      case .definition:
+        return .disabled
+      case .operationId:
+        return .persistedOperationsOnly
+      case [.operationId, .definition]:
+        return .automaticallyPersist
+      default:
+        return .disabled
+      }
     }
-  }
   
   /// Formatting of the GraphQL query string literal that is included in each
   /// generated operation object.
@@ -1436,7 +1411,7 @@ private struct AnyCodingKey: CodingKey {
   }
 }
 
-private func throwIfContainsUnexpectedKey<T, C: CodingKey & CaseIterable>(
+func throwIfContainsUnexpectedKey<T, C: CodingKey & CaseIterable>(
   container: KeyedDecodingContainer<C>,
   type: T.Type,
   decoder: Decoder
diff --git a/Sources/ApolloCodegenLib/CodegenConfiguration/ApolloCodegenConfiguration+OperationManifestConfiguration.swift b/Sources/ApolloCodegenLib/CodegenConfiguration/ApolloCodegenConfiguration+OperationManifestConfiguration.swift
new file mode 100644
index 0000000000..fef96343b7
--- /dev/null
+++ b/Sources/ApolloCodegenLib/CodegenConfiguration/ApolloCodegenConfiguration+OperationManifestConfiguration.swift
@@ -0,0 +1,91 @@
+import Foundation
+
+extension ApolloCodegenConfiguration {
+  
+  public struct OperationManifestConfiguration: Codable, Equatable {
+    
+    // MARK: - Properties
+    
+    /// Local path where the generated operation manifest file should be written.
+    public let path: String
+    /// The version format to use when generating the operation manifest. Defaults to `.persistedQueries`.
+    public let version: Version
+
+    public enum Version: String, Codable, Equatable {
+      /// Generates an operation manifest for use with persisted queries.
+      case persistedQueries
+      /// Generates an operation manifest in the legacy safelisting format used prior to the
+      /// [Persisted Queries](https://www.apollographql.com/docs/ios/fetching/persisted-queries) feature.
+      case legacy
+    }
+    
+    /// If set to `true` will generate the operation manifest every time code generation is run. Defaults to `false`
+    public let generateManifestOnCodeGeneration: Bool
+    
+    /// Default property values
+    public struct Default {
+      public static let version: Version = .persistedQueries
+      public static let generateManifestOnCodeGeneration: Bool = false
+    }
+    
+    // MARK: - Initializers
+    
+    /// Designated initializer
+    ///
+    /// - Parameters:
+    ///   - path: Local path where the generated operation manifest file should be written.
+    ///   - version: The version format to use when generating the operation manifest. Defaults to `.persistedQueries`.
+    ///   - generateManifestOnCodeGeneration: Whether or nor the operation manifest should be generated whenever code generation is run. Defaults to `false`.
+    public init(
+      path: String,
+      version: Version = Default.version,
+      generateManifestOnCodeGeneration: Bool = Default.generateManifestOnCodeGeneration
+    ) {
+      self.path = path
+      self.version = version
+      self.generateManifestOnCodeGeneration = generateManifestOnCodeGeneration
+    }
+    
+    // MARK: - Codable
+    
+    enum CodingKeys: CodingKey, CaseIterable {
+      case path
+      case version
+      case generateManifestOnCodeGeneration
+    }
+    
+    public init(from decoder: Decoder) throws {
+      let values = try decoder.container(keyedBy: CodingKeys.self)
+      try throwIfContainsUnexpectedKey(
+        container: values,
+        type: Self.self,
+        decoder: decoder
+      )
+      
+      path = try values.decode(
+        String.self,
+        forKey: .path
+      )
+      
+      version = try values.decode(
+        Version.self,
+        forKey: .version
+      )
+      
+      generateManifestOnCodeGeneration = try values.decode(
+        Bool.self,
+        forKey: .generateManifestOnCodeGeneration
+      )
+    }
+    
+    public func encode(to encoder: Encoder) throws {
+      var container = encoder.container(keyedBy: CodingKeys.self)
+      
+      try container.encode(self.path, forKey: .path)
+      try container.encode(self.version, forKey: .version)
+      try container.encode(self.generateManifestOnCodeGeneration, forKey: .generateManifestOnCodeGeneration)
+    }
+    
+  }
+  
+}
diff --git a/Sources/ApolloCodegenLib/FileGenerators/OperationManifestFileGenerator.swift b/Sources/ApolloCodegenLib/FileGenerators/OperationManifestFileGenerator.swift
index e0fb47485e..6db47952e1 100644
--- a/Sources/ApolloCodegenLib/FileGenerators/OperationManifestFileGenerator.swift
+++ b/Sources/ApolloCodegenLib/FileGenerators/OperationManifestFileGenerator.swift
@@ -37,7 +37,7 @@ struct OperationManifestFileGenerator {
   /// Parameters:
   ///  - config: A configuration object specifying output behavior.
   init?(config: ApolloCodegen.ConfigurationContext) {
-    guard config.output.operationManifest != nil else {
+    guard config.operationManifest != nil else {
       return nil
     }
 
@@ -57,7 +57,7 @@ struct OperationManifestFileGenerator {
   func generate(fileManager: ApolloFileManager = .default) throws {
     let rendered: String = try template.render(operations: operationManifest)
 
-    var manifestPath = config.output.operationManifest.unsafelyUnwrapped.path
+    var manifestPath = config.operationManifest.unsafelyUnwrapped.path
     let relativePrefix = "./"
       
     // if path begins with './' the path should be relative to the config.rootURL
@@ -80,10 +80,10 @@ struct OperationManifestFileGenerator {
   }
 
   var template: any OperationManifestTemplate {
-    switch config.output.operationManifest.unsafelyUnwrapped.version {
+    switch config.operationManifest.unsafelyUnwrapped.version {
     case .persistedQueries:
       return PersistedQueriesOperationManifestTemplate(config: config)
-    case .legacyAPQ:
+    case .legacy:
       return LegacyAPQOperationManifestTemplate()
     }
   }
diff --git a/Sources/CodegenCLI/Commands/FetchSchema.swift b/Sources/CodegenCLI/Commands/FetchSchema.swift
index df6bf2c108..061f223f96 100644
--- a/Sources/CodegenCLI/Commands/FetchSchema.swift
+++ b/Sources/CodegenCLI/Commands/FetchSchema.swift
@@ -28,32 +28,26 @@ public struct FetchSchema: ParsableCommand {
   ) throws {
     logger.SetLoggingLevel(verbose: inputs.verbose)
 
-    switch (inputs.string, inputs.path) {
-    case let (.some(string), _):
-      try fetchSchema(data: try string.asData(), schemaDownloadProvider: schemaDownloadProvider)
-
-    case let (nil, path):
-      let data = try fileManager.unwrappedContents(atPath: path)
-      try fetchSchema(data: data, schemaDownloadProvider: schemaDownloadProvider)
-    }
+    try fetchSchema(
+      configuration: inputs.getCodegenConfiguration(fileManager: fileManager),
+      schemaDownloadProvider: schemaDownloadProvider
+    )    
   }
 
   private func fetchSchema(
-    data: Data,
+    configuration codegenConfiguration: ApolloCodegenConfiguration,
     schemaDownloadProvider: SchemaDownloadProvider.Type
   ) throws {
-    let codegenConfiguration = try JSONDecoder().decode(ApolloCodegenConfiguration.self, from: data)
-
-    guard let schemaDownloadConfiguration = codegenConfiguration.schemaDownloadConfiguration else {
+    guard let schemaDownload = codegenConfiguration.schemaDownload else {
       throw Error(errorDescription: """
-        Missing schema download configuration. Hint: check the `schemaDownloadConfiguration` \
+        Missing schema download configuration. Hint: check the `schemaDownload` \
         property of your configuration.
         """
       )
     }
 
     try schemaDownloadProvider.fetch(
-      configuration: schemaDownloadConfiguration,
+      configuration: schemaDownload,
       withRootURL: rootOutputURL(for: inputs)
     )
   }
diff --git a/Sources/CodegenCLI/Commands/Generate.swift b/Sources/CodegenCLI/Commands/Generate.swift
index d6006c19f2..270c9a08d9 100644
--- a/Sources/CodegenCLI/Commands/Generate.swift
+++ b/Sources/CodegenCLI/Commands/Generate.swift
@@ -38,49 +38,47 @@ public struct Generate: ParsableCommand {
       with: inputs
     )
 
-    switch (inputs.string, inputs.path) {
-    case let (.some(string), _):
-      try generate(
-        data: try string.asData(),
-        codegenProvider: codegenProvider,
-        schemaDownloadProvider: schemaDownloadProvider
-      )
-
-    case let (nil, path):
-      let data = try fileManager.unwrappedContents(atPath: path)
-      try generate(
-        data: data,
-        codegenProvider: codegenProvider,
-        schemaDownloadProvider: schemaDownloadProvider
-      )
-    }
+    try generate(
+      configuration: inputs.getCodegenConfiguration(fileManager: fileManager),
+      codegenProvider: codegenProvider,
+      schemaDownloadProvider: schemaDownloadProvider
+    )
   }
 
   private func generate(
-    data: Data,
+    configuration: ApolloCodegenConfiguration,
     codegenProvider: CodegenProvider.Type,
     schemaDownloadProvider: SchemaDownloadProvider.Type
   ) throws {
-    let configuration = try JSONDecoder().decode(ApolloCodegenConfiguration.self, from: data)
-
     if fetchSchema {
       guard
-        let schemaDownloadConfiguration = configuration.schemaDownloadConfiguration
+        let schemaDownload = configuration.schemaDownload
       else {
         throw Error(errorDescription: """
-          Missing schema download configuration. Hint: check the `schemaDownloadConfiguration` \
+          Missing schema download configuration. Hint: check the `schemaDownload` \
           property of your configuration.
           """
         )
       }
 
       try fetchSchema(
-        configuration: schemaDownloadConfiguration,
+        configuration: schemaDownload,
         schemaDownloadProvider: schemaDownloadProvider
       )
     }
+    
+    var itemsToGenerate: ApolloCodegen.ItemsToGenerate = .code
+        
+    if let operationManifest = configuration.operationManifest,
+        operationManifest.generateManifestOnCodeGeneration {
+      itemsToGenerate.insert(.operationManifest)
+    }
 
-    try codegenProvider.build(with: configuration, withRootURL: rootOutputURL(for: inputs))
+    try codegenProvider.build(
+      with: configuration,
+      withRootURL: rootOutputURL(for: inputs),
+      itemsToGenerate: itemsToGenerate
+    )
   }
 
   private func fetchSchema(
diff --git a/Sources/CodegenCLI/Commands/GenerateOperationManifest.swift b/Sources/CodegenCLI/Commands/GenerateOperationManifest.swift
index faef37325f..2b695766cc 100644
--- a/Sources/CodegenCLI/Commands/GenerateOperationManifest.swift
+++ b/Sources/CodegenCLI/Commands/GenerateOperationManifest.swift
@@ -9,9 +9,9 @@ public struct GenerateOperationManifest: ParsableCommand {
   public static var configuration = CommandConfiguration(
     abstract: "Generate Persisted Queries operation manifest based on a code generation configuration."
   )
-  
+
   @OptionGroup var inputs: InputOptions
-  
+
   // MARK: - Implementation
   
   public init() { }
@@ -26,36 +26,39 @@ public struct GenerateOperationManifest: ParsableCommand {
     logger: LogLevelSetter.Type = CodegenLogger.self
   ) throws {
     logger.SetLoggingLevel(verbose: inputs.verbose)
-    
-    try checkForCLIVersionMismatch(
-      with: inputs
+
+    let configuration = try inputs.getCodegenConfiguration(fileManager: fileManager)
+
+    try validate(configuration: configuration)
+
+    try generateManifest(
+      configuration: configuration,
+      codegenProvider: codegenProvider
     )
-    
-    switch (inputs.string, inputs.path) {
-    case let (.some(string), _):
-      try generateManifest(
-        data: try string.asData(),
-        codegenProvider: codegenProvider
-      )
-    case let (nil, path):
-      try generateManifest(
-        data: try fileManager.unwrappedContents(atPath: path),
-        codegenProvider: codegenProvider
-      )
-    }
   }
   
   private func generateManifest(
-    data: Data,
+    configuration: ApolloCodegenConfiguration,
     codegenProvider: CodegenProvider.Type
   ) throws {
-    let configuration = try JSONDecoder().decode(ApolloCodegenConfiguration.self, from: data)
-    
-    try codegenProvider.generateOperationManifest(
+    try codegenProvider.build(
       with: configuration,
       withRootURL: rootOutputURL(for: inputs),
-      fileManager: .default
+      itemsToGenerate: [.operationManifest]
     )
   }
+
+  // MARK: - Validation
+
+  func validate(configuration: ApolloCodegenConfiguration) throws {
+    try checkForCLIVersionMismatch(with: inputs)
+
+    guard configuration.operationManifest != nil else {
+      throw ValidationError("""
+          `operationManifest` section must be set in the codegen configuration JSON in order
+          to generate an operation manifest.
+          """)
+    }
+  }
   
 }
diff --git a/Sources/CodegenCLI/OptionGroups/InputOptions.swift b/Sources/CodegenCLI/OptionGroups/InputOptions.swift
index d076b466b3..107d54d99b 100644
--- a/Sources/CodegenCLI/OptionGroups/InputOptions.swift
+++ b/Sources/CodegenCLI/OptionGroups/InputOptions.swift
@@ -1,4 +1,6 @@
+import Foundation
 import ArgumentParser
+import ApolloCodegenLib
 
 /// Shared group of common arguments used in commands for input parameters.
 struct InputOptions: ParsableArguments {
@@ -28,4 +30,16 @@ struct InputOptions: ParsableArguments {
     help: "Ignore Apollo version mismatch errors. Warning: This may lead to incompatible generated objects."
   )
   var ignoreVersionMismatch: Bool = false
+
+  func getCodegenConfiguration(fileManager: FileManager) throws -> ApolloCodegenConfiguration {
+    var data: Data
+    switch (string, path) {
+    case let (.some(string), _):
+      data = try string.asData()
+
+    case let (nil, path):
+      data = try fileManager.unwrappedContents(atPath: path)
+    }
+    return try JSONDecoder().decode(ApolloCodegenConfiguration.self, from: data)
+  }
 }
diff --git a/Sources/CodegenCLI/Protocols/CodegenProvider.swift b/Sources/CodegenCLI/Protocols/CodegenProvider.swift
index 9ed7051781..96ad36a103 100644
--- a/Sources/CodegenCLI/Protocols/CodegenProvider.swift
+++ b/Sources/CodegenCLI/Protocols/CodegenProvider.swift
@@ -4,14 +4,9 @@ import ApolloCodegenLib
 /// Generic representation of a code generation provider.
 public protocol CodegenProvider {
   static func build(
-    with configuration: ApolloCodegenConfiguration,
-    withRootURL rootURL: URL?
-  ) throws
-  
-  static func generateOperationManifest(
     with configuration: ApolloCodegenConfiguration,
     withRootURL rootURL: URL?,
-    fileManager: ApolloFileManager
+    itemsToGenerate: ApolloCodegen.ItemsToGenerate
   ) throws
 }
 
diff --git a/Tests/ApolloCodegenInternalTestHelpers/MockApolloCodegenConfiguration.swift b/Tests/ApolloCodegenInternalTestHelpers/MockApolloCodegenConfiguration.swift
index 7291d577ac..393a7d60ed 100644
--- a/Tests/ApolloCodegenInternalTestHelpers/MockApolloCodegenConfiguration.swift
+++ b/Tests/ApolloCodegenInternalTestHelpers/MockApolloCodegenConfiguration.swift
@@ -14,14 +14,16 @@ extension ApolloCodegenConfiguration {
       )
     ),
     options: OutputOptions = .init(schemaDocumentation: .exclude),
-    experimentalFeatures: ExperimentalFeatures = .init()
+    experimentalFeatures: ExperimentalFeatures = .init(),
+    operationManifest: OperationManifestConfiguration? = nil
   ) -> Self {
     .init(
       schemaNamespace: schemaNamespace,
       input: input,
       output: output,
       options: options,
-      experimentalFeatures: experimentalFeatures
+      experimentalFeatures: experimentalFeatures,
+      operationManifest: operationManifest
     )
   }
 
diff --git a/Tests/ApolloCodegenTests/ApolloCodegenConfigurationCodableTests.swift b/Tests/ApolloCodegenTests/ApolloCodegenConfigurationCodableTests.swift
index 50d8d18153..4545a7459a 100644
--- a/Tests/ApolloCodegenTests/ApolloCodegenConfigurationCodableTests.swift
+++ b/Tests/ApolloCodegenTests/ApolloCodegenConfigurationCodableTests.swift
@@ -35,8 +35,7 @@ class ApolloCodegenConfigurationCodableTests: XCTestCase {
             moduleType: .embeddedInTarget(name: "SomeTarget", accessModifier: .public)
           ),
           operations: .absolute(path: "/absolute/path", accessModifier: .internal),
-          testMocks: .swiftPackage(targetName: "SchemaTestMocks"),
-          operationManifest: .init(path: "/operation/identifiers/path")
+          testMocks: .swiftPackage(targetName: "SchemaTestMocks")
         ),
         options: .init(
           additionalInflectionRules: [
@@ -44,7 +43,6 @@ class ApolloCodegenConfigurationCodableTests: XCTestCase {
           ],
           deprecatedEnumCases: .exclude,
           schemaDocumentation: .exclude,
-          operationDocumentFormat: .definition,
           cocoapodsCompatibleImportStatements: true,
           warningsOnDeprecatedUsage: .exclude,
           conversionStrategies:.init(enumCases: .none),
@@ -53,6 +51,11 @@ class ApolloCodegenConfigurationCodableTests: XCTestCase {
         experimentalFeatures: .init(
           clientControlledNullability: true,
           legacySafelistingCompatibleOperations: true
+        ),
+        operationManifest: .init(
+          path: "/operation/identifiers/path",
+          version: .persistedQueries,
+          generateManifestOnCodeGeneration: false
         )
       )
     }
@@ -72,6 +75,11 @@ class ApolloCodegenConfigurationCodableTests: XCTestCase {
             "/path/to/schema.graphqls"
           ]
         },
+        "operationManifest" : {
+          "generateManifestOnCodeGeneration" : false,
+          "path" : "/operation/identifiers/path",
+          "version" : "persistedQueries"
+        },
         "options" : {
           "additionalInflectionRules" : [
             {
@@ -97,10 +105,6 @@ class ApolloCodegenConfigurationCodableTests: XCTestCase {
           "warningsOnDeprecatedUsage" : "exclude"
         },
         "output" : {
-          "operationManifest" : {
-            "path" : "/operation/identifiers/path",
-            "version" : "persistedQueries"
-          },
           "operations" : {
             "absolute" : {
               "accessModifier" : "internal",
diff --git a/Tests/ApolloCodegenTests/ApolloCodegenConfigurationTests.swift b/Tests/ApolloCodegenTests/ApolloCodegenConfigurationTests.swift
index 0472fc75ab..9229f2231b 100644
--- a/Tests/ApolloCodegenTests/ApolloCodegenConfigurationTests.swift
+++ b/Tests/ApolloCodegenTests/ApolloCodegenConfigurationTests.swift
@@ -69,7 +69,6 @@ class ApolloCodegenConfigurationTests: XCTestCase {
     )
 
     // then
-    expect(output.operationManifest).to(beNil())
     expect(output.operations).to(equal(.inSchemaModule))
   }
 
@@ -85,6 +84,5 @@ class ApolloCodegenConfigurationTests: XCTestCase {
     expect(config.options.additionalInflectionRules).to(beEmpty())
     expect(config.options.deprecatedEnumCases).to(equal(.include))
     expect(config.options.schemaDocumentation).to(equal(.include))
-    expect(config.options.operationDocumentFormat).to(equal([.definition]))
   }
 }
diff --git a/Tests/ApolloCodegenTests/ApolloCodegenTests.swift b/Tests/ApolloCodegenTests/ApolloCodegenTests.swift
index 09633f3f9a..8fe421e4e6 100644
--- a/Tests/ApolloCodegenTests/ApolloCodegenTests.swift
+++ b/Tests/ApolloCodegenTests/ApolloCodegenTests.swift
@@ -671,7 +671,8 @@ class ApolloCodegenTests: XCTestCase {
       compilationResult: compilationResult,
       ir: ir,
       config: config,
-      fileManager: fileManager
+      fileManager: fileManager,
+      itemsToGenerate: [.code]
     )
 
     // then
@@ -768,7 +769,8 @@ class ApolloCodegenTests: XCTestCase {
       compilationResult: compilationResult,
       ir: ir,
       config: config,
-      fileManager: fileManager
+      fileManager: fileManager,
+      itemsToGenerate: [.code]
     )
 
     // then
@@ -871,7 +873,8 @@ class ApolloCodegenTests: XCTestCase {
       compilationResult: compilationResult,
       ir: ir,
       config: config,
-      fileManager: fileManager
+      fileManager: fileManager,
+      itemsToGenerate: [.code]
     )
 
     // then
@@ -935,7 +938,8 @@ class ApolloCodegenTests: XCTestCase {
       compilationResult: compilationResult,
       ir: ir,
       config: config,
-      fileManager: fileManager
+      fileManager: fileManager,
+      itemsToGenerate: [.code]
     )
 
     // then
@@ -1037,7 +1041,8 @@ class ApolloCodegenTests: XCTestCase {
       compilationResult: compilationResult,
       ir: ir,
       config: config,
-      fileManager: fileManager
+      fileManager: fileManager,
+      itemsToGenerate: [.code]
     )
 
     // then
@@ -1137,7 +1142,8 @@ class ApolloCodegenTests: XCTestCase {
       compilationResult: compilationResult,
       ir: ir,
       config: config,
-      fileManager: fileManager
+      fileManager: fileManager,
+      itemsToGenerate: [.code]
     )
 
     // then
@@ -1184,7 +1190,7 @@ class ApolloCodegenTests: XCTestCase {
       options: .init(pruneGeneratedFiles: false)
     )
 
-    try ApolloCodegen.build(with: config, rootURL: directoryURL)
+    try ApolloCodegen.build(with: config, withRootURL: directoryURL)
 
     // then
     expect(ApolloFileManager.default.doesFileExist(atPath: testFile)).to(beTrue())
@@ -1241,7 +1247,7 @@ class ApolloCodegenTests: XCTestCase {
       )
     )
 
-    try ApolloCodegen.build(with: config, rootURL: directoryURL)
+    try ApolloCodegen.build(with: config, withRootURL: directoryURL)
 
     // then
     expect(ApolloFileManager.default.doesFileExist(atPath: testFile)).to(beFalse())
@@ -1295,7 +1301,7 @@ class ApolloCodegenTests: XCTestCase {
       )
     )
 
-    try ApolloCodegen.build(with: config, rootURL: directoryURL)
+    try ApolloCodegen.build(with: config, withRootURL: directoryURL)
 
     // then
     expect(ApolloFileManager.default.doesFileExist(atPath: testFile)).to(beFalse())
@@ -1364,7 +1370,7 @@ class ApolloCodegenTests: XCTestCase {
       )
     )
 
-    try ApolloCodegen.build(with: config, rootURL: directoryURL)
+    try ApolloCodegen.build(with: config, withRootURL: directoryURL)
 
     // then
     expect(ApolloFileManager.default.doesFileExist(atPath: testGeneratedFileInRootPath)).to(beFalse())
@@ -1437,7 +1443,7 @@ class ApolloCodegenTests: XCTestCase {
       )
     )
 
-    try ApolloCodegen.build(with: config, rootURL: directoryURL)
+    try ApolloCodegen.build(with: config, withRootURL: directoryURL)
 
     // then
     expect(ApolloFileManager.default.doesFileExist(atPath: testGeneratedFileInRootPath)).to(beFalse())
@@ -1495,13 +1501,13 @@ class ApolloCodegenTests: XCTestCase {
     // then
     
     // running codegen multiple times to validate symlink related file creation/deletion bug
-    try ApolloCodegen.build(with: config, rootURL: directoryURL)
+    try ApolloCodegen.build(with: config, withRootURL: directoryURL)
     expect(ApolloFileManager.default.doesFileExist(atPath: fileValidationPath)).to(beTrue())
     
-    try ApolloCodegen.build(with: config, rootURL: directoryURL)
+    try ApolloCodegen.build(with: config, withRootURL: directoryURL)
     expect(ApolloFileManager.default.doesFileExist(atPath: fileValidationPath)).to(beTrue())
     
-    try ApolloCodegen.build(with: config, rootURL: directoryURL)
+    try ApolloCodegen.build(with: config, withRootURL: directoryURL)
     expect(ApolloFileManager.default.doesFileExist(atPath: fileValidationPath)).to(beTrue())
 
   }
@@ -1586,7 +1592,7 @@ class ApolloCodegenTests: XCTestCase {
       )
     )
 
-    try ApolloCodegen.build(with: config, rootURL: directoryURL)
+    try ApolloCodegen.build(with: config, withRootURL: directoryURL)
 
     // then
     expect(ApolloFileManager.default.doesFileExist(atPath: testGeneratedFileInRootPath)).to(beTrue())
@@ -1694,7 +1700,7 @@ class ApolloCodegenTests: XCTestCase {
       )
     )
 
-    try ApolloCodegen.build(with: config, rootURL: directoryURL)
+    try ApolloCodegen.build(with: config, withRootURL: directoryURL)
 
     // then
     expect(ApolloFileManager.default.doesFileExist(atPath: testGeneratedFileInRootPath)).to(beTrue())
@@ -1796,7 +1802,7 @@ class ApolloCodegenTests: XCTestCase {
       )
     )
 
-    try ApolloCodegen.build(with: config, rootURL: directoryURL)
+    try ApolloCodegen.build(with: config, withRootURL: directoryURL)
 
     // then
     expect(ApolloFileManager.default.doesFileExist(atPath: testGeneratedFileInRootPath)).to(beTrue())
@@ -1861,7 +1867,7 @@ class ApolloCodegenTests: XCTestCase {
       )
     )
 
-    try ApolloCodegen.build(with: config, rootURL: directoryURL)
+    try ApolloCodegen.build(with: config, withRootURL: directoryURL)
 
     // then
     expect(ApolloFileManager.default.doesFileExist(atPath: testFile)).to(beFalse())
@@ -1917,7 +1923,7 @@ class ApolloCodegenTests: XCTestCase {
       )
     )
 
-    try ApolloCodegen.build(with: config, rootURL: directoryURL)
+    try ApolloCodegen.build(with: config, withRootURL: directoryURL)
 
     // then
     expect(ApolloFileManager.default.doesFileExist(atPath: testInTestMocksFolderFile)).to(beFalse())
@@ -1975,7 +1981,7 @@ class ApolloCodegenTests: XCTestCase {
       )
     )
 
-    try ApolloCodegen.build(with: config, rootURL: directoryURL)
+    try ApolloCodegen.build(with: config, withRootURL: directoryURL)
 
     // then
     expect(ApolloFileManager.default.doesFileExist(atPath: testInTestMocksFolderFile)).to(beFalse())
diff --git a/Tests/ApolloCodegenTests/CodeGeneration/FileGenerators/OperationManifestFileGeneratorTests.swift b/Tests/ApolloCodegenTests/CodeGeneration/FileGenerators/OperationManifestFileGeneratorTests.swift
index f9bc46aff0..5237fc2fcf 100644
--- a/Tests/ApolloCodegenTests/CodeGeneration/FileGenerators/OperationManifestFileGeneratorTests.swift
+++ b/Tests/ApolloCodegenTests/CodeGeneration/FileGenerators/OperationManifestFileGeneratorTests.swift
@@ -22,9 +22,9 @@ class OperationManifestFileGeneratorTests: XCTestCase {
 
   private func buildSubject(
     path: String? = nil,
-    version: ApolloCodegenConfiguration.OperationManifestFileOutput.Version = .legacyAPQ
+    version: ApolloCodegenConfiguration.OperationManifestConfiguration.Version = .legacy
   ) throws {
-    let manifest: ApolloCodegenConfiguration.OperationManifestFileOutput? = {
+    let manifest: ApolloCodegenConfiguration.OperationManifestConfiguration? = {
       guard let path else { return nil }
       return .init(path: path, version: version)
     }()
@@ -32,9 +32,9 @@ class OperationManifestFileGeneratorTests: XCTestCase {
     subject = try OperationManifestFileGenerator(
       config: ApolloCodegen.ConfigurationContext(config: ApolloCodegenConfiguration.mock(
         output: .init(
-          schemaTypes: .init(path: "", moduleType: .swiftPackageManager),
-          operationManifest: manifest
-        )
+          schemaTypes: .init(path: "", moduleType: .swiftPackageManager)
+        ),
+        operationManifest: manifest
       ))
     ).xctUnwrapped()
   }
@@ -43,10 +43,14 @@ class OperationManifestFileGeneratorTests: XCTestCase {
 
   func test__initializer__givenPath_shouldReturnInstance() {
     // given
-    let config = ApolloCodegenConfiguration.mock(output: .init(
-      schemaTypes: .init(path: "", moduleType: .swiftPackageManager),
-      operationManifest: .init(path: "a/file/path")
-    ))
+    let config = ApolloCodegenConfiguration.mock(
+      output: .init(
+        schemaTypes: .init(path: "", moduleType: .swiftPackageManager)
+      ),
+      operationManifest: .init(
+        path: "a/file/path"
+      )
+    )
 
     // when
     let instance = OperationManifestFileGenerator(config: .init(config: config))
@@ -57,10 +61,12 @@ class OperationManifestFileGeneratorTests: XCTestCase {
 
   func test__initializer__givenNilPath_shouldReturnNil() {
     // given
-    let config = ApolloCodegenConfiguration.mock(output: .init(
-      schemaTypes: .init(path: "", moduleType: .swiftPackageManager),
+    let config = ApolloCodegenConfiguration.mock(
+      output: .init(
+        schemaTypes: .init(path: "", moduleType: .swiftPackageManager)
+      ),
       operationManifest: nil
-    ))
+    )
 
     // when
     let instance = OperationManifestFileGenerator(config: .init(config: config))
@@ -267,9 +273,9 @@ class OperationManifestFileGeneratorTests: XCTestCase {
 
   // MARK: - Template Type Selection Tests
 
-  func test__template__givenOperationManifestVersion_apqLegacy__isLegacyAPQTemplate() throws {
+  func test__template__givenOperationManifestVersion_legacy__isLegacyTemplate() throws {
     // given
-    try buildSubject(path: "a/path", version: .legacyAPQ)
+    try buildSubject(path: "a/path", version: .legacy)
 
     // when
     let actual = subject.template
diff --git a/Tests/CodegenCLITests/Commands/FetchSchemaTests.swift b/Tests/CodegenCLITests/Commands/FetchSchemaTests.swift
index eee003df56..d2d52921fe 100644
--- a/Tests/CodegenCLITests/Commands/FetchSchemaTests.swift
+++ b/Tests/CodegenCLITests/Commands/FetchSchemaTests.swift
@@ -48,7 +48,7 @@ class FetchSchemaTests: XCTestCase {
 
     var didCallFetch = false
     MockApolloSchemaDownloader.fetchHandler = { configuration in
-      expect(configuration).to(equal(mockConfiguration.schemaDownloadConfiguration))
+      expect(configuration).to(equal(mockConfiguration.schemaDownload))
 
       didCallFetch = true
     }
@@ -80,7 +80,7 @@ class FetchSchemaTests: XCTestCase {
 
     var didCallFetch = false
     MockApolloSchemaDownloader.fetchHandler = { configuration in
-      expect(configuration).to(equal(mockConfiguration.schemaDownloadConfiguration))
+      expect(configuration).to(equal(mockConfiguration.schemaDownload))
 
       didCallFetch = true
     }
@@ -110,7 +110,7 @@ class FetchSchemaTests: XCTestCase {
 
     var didCallFetch = false
     MockApolloSchemaDownloader.fetchHandler = { configuration in
-      expect(configuration).to(equal(mockConfiguration.schemaDownloadConfiguration))
+      expect(configuration).to(equal(mockConfiguration.schemaDownload))
 
       didCallFetch = true
     }
diff --git a/Tests/CodegenCLITests/Commands/GenerateOperationManifestTests.swift b/Tests/CodegenCLITests/Commands/GenerateOperationManifestTests.swift
index a035cd5933..20fdff8b0d 100644
--- a/Tests/CodegenCLITests/Commands/GenerateOperationManifestTests.swift
+++ b/Tests/CodegenCLITests/Commands/GenerateOperationManifestTests.swift
@@ -3,7 +3,6 @@ import Nimble
 import ApolloInternalTestHelpers
 @testable import CodegenCLI
 import ApolloCodegenLib
-import ArgumentParser
 
 class GenerateOperationManifestTests: XCTestCase {
 
diff --git a/Tests/CodegenCLITests/Commands/GenerateTests.swift b/Tests/CodegenCLITests/Commands/GenerateTests.swift
index 773589ef62..b5230a328e 100644
--- a/Tests/CodegenCLITests/Commands/GenerateTests.swift
+++ b/Tests/CodegenCLITests/Commands/GenerateTests.swift
@@ -144,7 +144,7 @@ class GenerateTests: XCTestCase {
 
     var didCallFetch = false
     MockApolloSchemaDownloader.fetchHandler = { configuration in
-      expect(configuration).to(equal(mockConfiguration.schemaDownloadConfiguration))
+      expect(configuration).to(equal(mockConfiguration.schemaDownload))
 
       didCallFetch = true
     }
@@ -185,7 +185,7 @@ class GenerateTests: XCTestCase {
 
     var didCallFetch = false
     MockApolloSchemaDownloader.fetchHandler = { configuration in
-      expect(configuration).to(equal(mockConfiguration.schemaDownloadConfiguration))
+      expect(configuration).to(equal(mockConfiguration.schemaDownload))
 
       didCallFetch = true
     }
@@ -234,7 +234,7 @@ class GenerateTests: XCTestCase {
 
     var didCallFetch = false
     MockApolloSchemaDownloader.fetchHandler = { configuration in
-      expect(configuration).to(equal(mockConfiguration.schemaDownloadConfiguration))
+      expect(configuration).to(equal(mockConfiguration.schemaDownload))
 
       didCallFetch = true
     }
diff --git a/Tests/CodegenCLITests/Support/MockApolloCodegen.swift b/Tests/CodegenCLITests/Support/MockApolloCodegen.swift
index d1ca6ac2f3..24592d7ba6 100644
--- a/Tests/CodegenCLITests/Support/MockApolloCodegen.swift
+++ b/Tests/CodegenCLITests/Support/MockApolloCodegen.swift
@@ -7,7 +7,8 @@ class MockApolloCodegen: CodegenProvider {
 
   static func build(
     with configuration: ApolloCodegenConfiguration,
-    withRootURL rootURL: URL?
+    withRootURL rootURL: URL?,
+    itemsToGenerate: ApolloCodegen.ItemsToGenerate
   ) throws {
     guard let handler = buildHandler else {
       fatalError("You must set buildHandler before calling \(#function)!")
@@ -20,19 +21,4 @@ class MockApolloCodegen: CodegenProvider {
     try handler(configuration)
   }
   
-  static func generateOperationManifest(
-    with configuration: ApolloCodegenLib.ApolloCodegenConfiguration,
-    withRootURL rootURL: URL?,
-    fileManager: ApolloCodegenLib.ApolloFileManager
-  ) throws {
-    guard let handler = buildHandler else {
-      fatalError("You must set buildHandler before calling \(#function)!")
-    }
-    
-    defer {
-      buildHandler = nil
-    }
-    
-    try handler(configuration)
-  }
 }
diff --git a/Tests/CodegenCLITests/Support/MockApolloCodegenConfiguration.swift b/Tests/CodegenCLITests/Support/MockApolloCodegenConfiguration.swift
index a337ab2a65..047adff770 100644
--- a/Tests/CodegenCLITests/Support/MockApolloCodegenConfiguration.swift
+++ b/Tests/CodegenCLITests/Support/MockApolloCodegenConfiguration.swift
@@ -9,15 +9,19 @@ extension ApolloCodegenConfiguration {
         schemaPath: "./schema.graphqls"
       ),
       output: .init(
-        schemaTypes: .init(path: ".", moduleType: .swiftPackageManager),
-        operationManifest: .init(path: "./manifest", version: .persistedQueries)
+        schemaTypes: .init(path: ".", moduleType: .swiftPackageManager)
       ),
       options: .init(
         operationDocumentFormat: [.definition, .operationId]
       ),
-      schemaDownloadConfiguration: .init(
+      schemaDownload: .init(
         using: .introspection(endpointURL: URL(string: "http://some.server")!),
         outputPath: "./schema.graphqls"
+      ),
+      operationManifest: .init(
+        path: "./manifest",
+        version: .persistedQueries,
+        generateManifestOnCodeGeneration: false
       )
     )
   }
diff --git a/docs/source/code-generation/codegen-configuration.mdx b/docs/source/code-generation/codegen-configuration.mdx
index a2afde1273..76972f2863 100644
--- a/docs/source/code-generation/codegen-configuration.mdx
+++ b/docs/source/code-generation/codegen-configuration.mdx
@@ -21,7 +21,8 @@ There are a number of base configuration properties, each representing a specifi
 | [`output`](#file-output) | Location and structure of the generated files and modules. |
 | [`options`](#output-options) | Rules and options to customize the generated code. |
 | [`experimentalFeatures`](#experimental-features) | Used to enable experimental features.<br/>*Note: These features could change at any time and are not guaranteed to always be available.* |
-| [`schemaDownloadConfiguration`](#schema-download-configuration) | Configuration to fetch a GraphQL schema before generation. |
+| [`schemaDownload`](#schema-download-configuration) | Configuration to fetch a GraphQL schema before generation. |
+| [`operationManifest`](#operation-manifest-configuration) | Configuration to generate operation manifests for persisted queries |
 
 ## Schema namespace
 
@@ -98,7 +99,6 @@ The properties to configure `output` are:
 | [`schemaTypes`](#schema-types) | Location and structure of the generated schema types files. |
 | [`operations`](#operations)    | Location and structure of the generated operation files such as queries, mutations, subscriptions, and fragments. |
 | [`testMocks`](#test-mocks)     | Location and structure of the test mock operation object files.<br/><br/>If `.none`, test mocks will not be generated. |
-| [`operationManifest`](#operation-manifest) | Configures the generation of an operation manifest JSON file for use with persisted queries or [Automatic Persisted Queries](../fetching/apqs). |
 
 <MultiCodeBlock>
 
@@ -395,42 +395,6 @@ Specify the directory for your test mocks using the `path` parameter. This is re
 >
 > Test mocks generated this way may also be manually embedded in a test utility module that is imported by your test target.
 
-### Operation Manifest
-
-Providing a value for this property will generate a JSON document with all your operations and their computed identifier hashes. This document can be used to pre-register the identifiers for your operations with a server that supports [persisted queries or Automatic Persisted Queries](./../fetching/apqs).
-
-The properties of the Operation Manifest configuration object are:
-
-| Property Name | Description |
-| ----- | ----------- |
-| `path` | Local path where the generated operation manifest file should be written. |
-| [`version`](https://www.apollographql.com/docs/ios/docc/documentation/apollocodegenlib/apollocodegenconfiguration/operationmanifestfileoutput/version) | The version format to use when generating the operation manifest. |
-
-<MultiCodeBlock>
-
-```json title="CLI Configuration JSON"
-"output": {
-	"operationManifest" : {
-		"path" : "./generated/operationIdentifiers.json",
-		"version" : "persistedQueries"
-	}
-}
-```
-
-```swift title="Swift Codegen Setup"
-let configuration = ApolloCodegenConfiguration(
-	// Other properties not shown
-	output: ApolloCodegenConfiguration.FileOutput(
-		operationManifest: .init(
-			path: "./generated/operationIdentifiers.json",
-			version: .persistedQueries
-		)
-	)
-)
-```
-
-</MultiCodeBlock>
-
 ## Output options
 
 The code generation engine supports a number of configuration options to change the behaviour of the generator and tailor the generated Swift code to your specific needs.
@@ -444,7 +408,7 @@ The top-level properties are:
 | [`deprecatedEnumCases`](https://www.apollographql.com/docs/ios/docc/documentation/apollocodegenlib/apollocodegenconfiguration/outputoptions/deprecatedenumcases) | Annotate generated Swift enums with the Swift `@available` attribute for GraphQL enum cases annotated with the built-in [`@deprecated` directive](https://spec.graphql.org/draft/#sec--deprecated). |
 | [`schemaDocumentation`](https://www.apollographql.com/docs/ios/docc/documentation/apollocodegenlib/apollocodegenconfiguration/outputoptions/schemadocumentation) | Include or exclude [schema documentation](https://spec.graphql.org/draft/#sec-Descriptions) in the generated files. |
 | [`selectionSetInitializers`](https://www.apollographql.com/docs/ios/docc/documentation/apollocodegenlib/apollocodegenconfiguration/outputoptions/selectionsetinitializers) | Generate initializers for your generated selection set models. |
-| [`operationDocumentFormat`](https://www.apollographql.com/docs/ios/docc/documentation/apollocodegenlib/apollocodegenconfiguration/outputoptions/operationdocumentformat) | How to generate the operation documents for your generated operations. This can be used to generate operation identifiers for use with a server that supports [persisted queries or Automatic Persisted Queries](./../fetching/apqs) |
+| [`operationDocumentFormat`](https://www.apollographql.com/docs/ios/docc/documentation/apollocodegenlib/apollocodegenconfiguration/outputoptions/operationdocumentformat) | How to generate the operation documents for your generated operations. This can be used to generate operation identifiers for use with a server that supports [Persisted Queries or Automatic Persisted Queries](./../fetching/persisted-queries) |
 | [`cocoapodsCompatibleImportStatements`](https://www.apollographql.com/docs/ios/docc/documentation/apollocodegenlib/apollocodegenconfiguration/outputoptions/cocoapodscompatibleimportstatements) | Generate import statements that are compatible with including `Apollo` via Cocoapods. |
 | [`warningsOnDeprecatedUsage`](https://www.apollographql.com/docs/ios/docc/documentation/apollocodegenlib/apollocodegenconfiguration/outputoptions/warningsondeprecatedusage) | Annotate generated Swift code with the Swift `@available` attribute and `@deprecated` argument for parts of the GraphQL schema annotated with the built-in [`@deprecated` directive](https://spec.graphql.org/draft/#sec--deprecated). |
 | [`conversionStrategies`](https://www.apollographql.com/docs/ios/docc/documentation/apollocodegenlib/apollocodegenconfiguration/outputoptions/conversionstrategies) | Rules for how to convert the names of values from the schema in generated code. |
@@ -579,7 +543,7 @@ The properties you will need to configure are:
 <MultiCodeBlock>
 
 ```json title="CLI Configuration JSON"
-"schemaDownloadConfiguration": {
+"schemaDownload": {
 	"downloadMethod": {
 		"apolloRegistry": {
 			"_0": {
@@ -601,7 +565,7 @@ The properties you will need to configure are:
 ```swift title="Swift Codegen Setup"
 let configuration = ApolloCodegenConfiguration(
   // Other properties not shown
-  schemaDownloadConfiguration: ApolloSchemaDownloadConfiguration(
+  schemaDownload: ApolloSchemaDownloadConfiguration(
     using: .apolloRegistry(.init(
       apiKey: "your-api-key",
       graphID: "your-graphid",
@@ -635,7 +599,7 @@ The properties you will need to configure are:
 <MultiCodeBlock>
 
 ```json title="CLI Configuration JSON"
-"schemaDownloadConfiguration": {
+"schemaDownload": {
 	"downloadMethod": {
 		"introspection": {
 			"endpointURL": "https://server.com",
@@ -655,7 +619,7 @@ The properties you will need to configure are:
 ```swift title="Swift Codegen Setup"
 let configuration = ApolloCodegenConfiguration(
 	// Other properties not shown
-	schemaDownloadConfiguration: ApolloSchemaDownloadConfiguration(
+	schemaDownload: ApolloSchemaDownloadConfiguration(
 		using: .introspection(
 			endpointURL: URL(string: "https://server.com")!),
 		timeout: 60.0,
@@ -667,3 +631,36 @@ let configuration = ApolloCodegenConfiguration(
 </MultiCodeBlock>
 
 For more details, see the section on [downloading a schema](./downloading-schema).
+
+## Operation Manifest Configuration
+
+Optional settings used to configure generation of the operation identifier manifest for use with [Persisted Queries](./../fetching/persisted-queries).
+
+| Property Name | Description |
+| ------------- | ----------- |
+| `path` | Local path where the generated operation manifest file should be written. |
+| [`version`](https://www.apollographql.com/docs/ios/docc/documentation/apollocodegenlib/apollocodegenconfiguration/operationmanifestfileoutput/version) | The version format to use when generating the operation manifest. |
+| [`generateManifestOnCodeGeneration`](https://www.apollographql.com/docs/ios/docc/documentation/apollocodegenlib/apollocodegenconfiguration/operationmanifestconfiguration/generateManifestOnCodeGeneration) | Whether or not the operation manifest should be generated every time code generation is run. Defaults to false. |
+
+<MultiCodeBlock>
+
+```json title="CLI Configuration JSON"
+"operationManifest" : {
+  "generateManifestOnCodeGeneration" : false,
+  "path" : "/operation/identifiers/path",
+  "version" : "persistedQueries"
+}
+```
+
+```swift title="Swift Codegen Setup"
+let configuration = ApolloCodegenConfiguration(
+    // Other properties not shown
+    operationManifest: .init(
+        path: "./manifest/operationManifest.json",
+        version: .persistedQueries,
+        generateManifestOnCodeGeneration: false
+    )
+)
+```
+
+</MultiCodeBlock>