diff --git a/src/BenchmarkDotNet/Templates/WasmCsProj.txt b/src/BenchmarkDotNet/Templates/WasmCsProj.txt
index 1910911fe0..e45f5c3789 100644
--- a/src/BenchmarkDotNet/Templates/WasmCsProj.txt
+++ b/src/BenchmarkDotNet/Templates/WasmCsProj.txt
@@ -23,6 +23,7 @@
     <RunAOTCompilation>$RUN_AOT$</RunAOTCompilation>
     <PublishTrimmed>$(RunAOTCompilation)</PublishTrimmed>
     <WasmGenerateRunV8Script>true</WasmGenerateRunV8Script>
+    <ErrorOnDuplicatePublishOutputFiles>false</ErrorOnDuplicatePublishOutputFiles>
     <ValidateExecutableReferencesMatchSelfContained>false</ValidateExecutableReferencesMatchSelfContained>
     <EnableDefaultWasmAssembliesToBundle>false</EnableDefaultWasmAssembliesToBundle>
     <StartupObject>BenchmarkDotNet.Autogenerated.UniqueProgramName</StartupObject>
diff --git a/src/BenchmarkDotNet/Toolchains/DotNetCli/DotNetCliCommand.cs b/src/BenchmarkDotNet/Toolchains/DotNetCli/DotNetCliCommand.cs
index 3d4f2fefd6..e9078f293f 100644
--- a/src/BenchmarkDotNet/Toolchains/DotNetCli/DotNetCliCommand.cs
+++ b/src/BenchmarkDotNet/Toolchains/DotNetCli/DotNetCliCommand.cs
@@ -1,5 +1,6 @@
 using System;
 using System.Collections.Generic;
+using System.IO;
 using System.Linq;
 using System.Text;
 using BenchmarkDotNet.Characteristics;
@@ -260,10 +261,11 @@ internal static StringBuilder MaybeAppendOutputPaths(this StringBuilder stringBu
             => excludeOutput
                 ? stringBuilder
                 : stringBuilder
-                    .AppendArgument($"/p:IntermediateOutputPath=\"{artifactsPaths.IntermediateDirectoryPath}\"\\")
-                    .AppendArgument($"/p:OutDir=\"{artifactsPaths.BinariesDirectoryPath}\"")
+                    // Use AltDirectorySeparatorChar so it's not interpreted as an escaped quote `\"`.
+                    .AppendArgument($"/p:IntermediateOutputPath=\"{artifactsPaths.IntermediateDirectoryPath}{Path.AltDirectorySeparatorChar}\"")
+                    .AppendArgument($"/p:OutDir=\"{artifactsPaths.BinariesDirectoryPath}{Path.AltDirectorySeparatorChar}\"")
                     // OutputPath is legacy, per-project version of OutDir. We set both just in case. https://github.com/dotnet/msbuild/issues/87
-                    .AppendArgument($"/p:OutputPath=\"{artifactsPaths.BinariesDirectoryPath}\"")
-                    .AppendArgument(isRestore ? string.Empty : $"--output \"{artifactsPaths.BinariesDirectoryPath}\"");
+                    .AppendArgument($"/p:OutputPath=\"{artifactsPaths.BinariesDirectoryPath}{Path.AltDirectorySeparatorChar}\"")
+                    .AppendArgument(isRestore ? string.Empty : $"--output \"{artifactsPaths.BinariesDirectoryPath}{Path.AltDirectorySeparatorChar}\"");
     }
 }
diff --git a/src/BenchmarkDotNet/Toolchains/GeneratorBase.cs b/src/BenchmarkDotNet/Toolchains/GeneratorBase.cs
index 0b3aea02cd..cab9d811c4 100644
--- a/src/BenchmarkDotNet/Toolchains/GeneratorBase.cs
+++ b/src/BenchmarkDotNet/Toolchains/GeneratorBase.cs
@@ -2,6 +2,7 @@
 using System.IO;
 using System.Text;
 using BenchmarkDotNet.Code;
+using BenchmarkDotNet.Extensions;
 using BenchmarkDotNet.Loggers;
 using BenchmarkDotNet.Portability;
 using BenchmarkDotNet.Running;
@@ -103,6 +104,7 @@ [PublicAPI] protected virtual void GenerateProject(BuildPartition buildPartition
         [PublicAPI] protected virtual void GenerateAppConfig(BuildPartition buildPartition, ArtifactsPaths artifactsPaths)
         {
             string sourcePath = buildPartition.AssemblyLocation + ".config";
+            artifactsPaths.AppConfigPath.EnsureFolderExists();
 
             using (var source = File.Exists(sourcePath) ? new StreamReader(File.OpenRead(sourcePath)) : TextReader.Null)
             using (var destination = new StreamWriter(File.Create(artifactsPaths.AppConfigPath), Encoding.UTF8))
diff --git a/src/BenchmarkDotNet/Toolchains/MonoWasm/WasmExecutor.cs b/src/BenchmarkDotNet/Toolchains/MonoWasm/WasmExecutor.cs
index 024c8e4242..7e857ff364 100644
--- a/src/BenchmarkDotNet/Toolchains/MonoWasm/WasmExecutor.cs
+++ b/src/BenchmarkDotNet/Toolchains/MonoWasm/WasmExecutor.cs
@@ -61,7 +61,7 @@ private static Process CreateProcess(BenchmarkCase benchmarkCase, ArtifactsPaths
             {
                 FileName = runtime.JavaScriptEngine,
                 Arguments = $"{runtime.JavaScriptEngineArguments} {mainJs} -- --run {artifactsPaths.ProgramName}.dll {args} ",
-                WorkingDirectory = artifactsPaths.BinariesDirectoryPath,
+                WorkingDirectory = Path.Combine(artifactsPaths.BinariesDirectoryPath, "AppBundle"),
                 UseShellExecute = false,
                 RedirectStandardOutput = true,
                 RedirectStandardInput = false, // not supported by WASM!
diff --git a/src/BenchmarkDotNet/Toolchains/MonoWasm/WasmGenerator.cs b/src/BenchmarkDotNet/Toolchains/MonoWasm/WasmGenerator.cs
index cc251abb0d..7c9aa8826f 100644
--- a/src/BenchmarkDotNet/Toolchains/MonoWasm/WasmGenerator.cs
+++ b/src/BenchmarkDotNet/Toolchains/MonoWasm/WasmGenerator.cs
@@ -66,9 +66,9 @@ protected void GenerateProjectFile(BuildPartition buildPartition, ArtifactsPaths
             File.WriteAllText(artifactsPaths.ProjectFilePath, content);
         }
 
-        protected override string GetExecutablePath(string binariesDirectoryPath, string programName) => Path.Combine(binariesDirectoryPath, MainJS);
+        protected override string GetExecutablePath(string binariesDirectoryPath, string programName) => Path.Combine(binariesDirectoryPath, "AppBundle", MainJS);
 
         protected override string GetBinariesDirectoryPath(string buildArtifactsDirectoryPath, string configuration)
-            => Path.Combine(buildArtifactsDirectoryPath, "bin", configuration, TargetFrameworkMoniker, "browser-wasm", "AppBundle");
+            => Path.Combine(buildArtifactsDirectoryPath, "bin", configuration, TargetFrameworkMoniker, "browser-wasm");
     }
 }