diff --git a/packages/cli-e2e/__tests__/orgResources.specs.ts b/packages/cli-e2e/__tests__/orgResources.specs.ts
index 69a56e6bff..eb4236ffd2 100644
--- a/packages/cli-e2e/__tests__/orgResources.specs.ts
+++ b/packages/cli-e2e/__tests__/orgResources.specs.ts
@@ -3,7 +3,7 @@ import {CLI_EXEC_PATH, getConfig, getPathToHomedirEnvFile} from '../utils/cli';
 import {ProcessManager} from '../utils/processManager';
 import {Terminal} from '../utils/terminal/terminal';
 import {config} from 'dotenv';
-import {ensureDirSync} from 'fs-extra';
+import {ensureDirSync, rmSync} from 'fs-extra';
 import PlatformClient, {FieldTypes} from '@coveord/platform-client';
 import {getPlatformClient} from '../utils/platform';
 import {readdirSync} from 'fs';
@@ -92,13 +92,16 @@ describe('org:resources', () => {
   const pullFromOrg = async (
     targetOrg: string,
     procManager: ProcessManager,
-    destinationPath: string
+    destinationPath: string,
+    additionalFlags: string[] = []
   ) => {
     const args: string[] = [
       CLI_EXEC_PATH,
       'org:resources:pull',
       `-t=${targetOrg}`,
+      '-o',
       '--no-git',
+      ...additionalFlags,
     ];
 
     const pullTerminal = createNewTerminal(
@@ -250,8 +253,11 @@ describe('org:resources', () => {
 
   describe('org:resources:pull', () => {
     const destinationPath = join('new-snapshot-project');
+    const getResourceFolderContent = (projectPath: string) =>
+      readdirSync(join(projectPath, 'resources'));
 
-    beforeAll(() => {
+    beforeEach(() => {
+      rmSync(destinationPath, {recursive: true, force: true});
       ensureDirSync(destinationPath);
     });
 
@@ -259,7 +265,6 @@ describe('org:resources', () => {
       "should pull the org's content",
       async () => {
         await pullFromOrg(testOrgId, processManager, destinationPath);
-
         const snapshotFiles = readdirSync(snapshotProjectPath);
         const destinationFiles = readdirSync(destinationPath);
 
@@ -267,6 +272,23 @@ describe('org:resources', () => {
       },
       defaultTimeout
     );
+
+    it(
+      'directory should only contains pulled resources',
+      async () => {
+        await pullFromOrg(testOrgId, processManager, destinationPath, [
+          '-r=field',
+        ]);
+        const originalResources = getResourceFolderContent(snapshotProjectPath);
+        const destinationResources = getResourceFolderContent(destinationPath);
+
+        expect(destinationResources.length).toBeGreaterThan(0);
+        expect(destinationResources.length).toBeLessThan(
+          originalResources.length
+        );
+      },
+      defaultTimeout
+    );
   });
 
   it('should not have any snapshot in the target org', async () => {
diff --git a/packages/cli/src/commands/org/resources/pull.ts b/packages/cli/src/commands/org/resources/pull.ts
index 2015c8007a..590b799acf 100644
--- a/packages/cli/src/commands/org/resources/pull.ts
+++ b/packages/cli/src/commands/org/resources/pull.ts
@@ -59,6 +59,11 @@ export default class Pull extends Command {
       default: true,
       allowNo: true,
     }),
+    overwrite: flags.boolean({
+      char: 'o',
+      description: 'Overwrite resources directory if it exists.',
+      default: false,
+    }),
   };
 
   public static hidden = true;
@@ -70,10 +75,13 @@ export default class Pull extends Command {
     HasNecessaryCoveoPrivileges(writeSnapshotPrivilege)
   )
   public async run() {
+    const project = new Project(this.projectPath);
+    await this.ensureProjectReset(project);
+
     const snapshot = await this.getSnapshot();
 
     cli.action.start('Updating project with Snapshot');
-    await this.refreshProject(snapshot);
+    await this.refreshProject(project, snapshot);
 
     await snapshot.delete();
     cli.action.stop('Project updated');
@@ -103,9 +111,8 @@ export default class Pull extends Command {
     }
   }
 
-  private async refreshProject(snapshot: Snapshot) {
+  private async refreshProject(project: Project, snapshot: Snapshot) {
     const {flags} = this.parse(Pull);
-    const project = new Project(this.projectPath);
     if (flags.git && !project.contains('.git')) {
       await spawnProcess('git', ['init', `${this.projectPath}`], {
         stdio: 'ignore',
@@ -115,6 +122,21 @@ export default class Pull extends Command {
     await project.refresh(snapshotBlob);
   }
 
+  private async ensureProjectReset(project: Project) {
+    const {flags} = this.parse(Pull);
+    if (!flags.overwrite && project.contains(Project.resourceFolderName)) {
+      const overwrite =
+        await cli.confirm(dedent`There is already a Coveo project with resources in it.
+        This command will overwrite the ${Project.resourceFolderName} folder content, do you want to proceed? (y/n)`);
+
+      if (!overwrite) {
+        this.exit();
+      }
+    }
+
+    project.reset();
+  }
+
   private async getSnapshot() {
     const {flags} = this.parse(Pull);
     const target = await getTargetOrg(this.configuration, flags.target);
diff --git a/packages/cli/src/lib/project/project.ts b/packages/cli/src/lib/project/project.ts
index 3f822ba2e9..940401d41d 100644
--- a/packages/cli/src/lib/project/project.ts
+++ b/packages/cli/src/lib/project/project.ts
@@ -4,6 +4,7 @@ import {
   readdirSync,
   unlinkSync,
   writeFileSync,
+  rmSync,
 } from 'fs';
 import {extname, join} from 'path';
 import {cli} from 'cli-ux';
@@ -14,7 +15,7 @@ import {DotFolder, DotFolderConfig} from './dotFolder';
 import {readJsonSync, writeJsonSync, WriteOptions} from 'fs-extra';
 
 export class Project {
-  private static readonly resourceFolderName = 'resources';
+  public static readonly resourceFolderName = 'resources';
   public static readonly jsonFormat: WriteOptions = {spaces: '\t'};
   public constructor(private _pathToProject: string) {
     if (!this.isCoveoProject) {
@@ -31,6 +32,12 @@ export class Project {
     this.deleteTemporaryZipFile();
   }
 
+  public reset() {
+    if (this.isResourcesProject) {
+      rmSync(Project.resourceFolderName, {recursive: true, force: true});
+    }
+  }
+
   private formatResourceFiles(dirPath = this.resourcePath) {
     const files = readdirSync(dirPath, {withFileTypes: true});
     files.forEach((file) => {
@@ -98,6 +105,7 @@ export class Project {
   public get resourcePath() {
     return join(this._pathToProject, Project.resourceFolderName);
   }
+
   public contains(fileName: string) {
     return existsSync(join(this.pathToProject, fileName));
   }