diff --git a/packages/cli/src/environments.ee/source-control/__tests__/source-control-export.service.test.ts b/packages/cli/src/environments.ee/source-control/__tests__/source-control-export.service.test.ts
index 016b25e802c..68984dfc394 100644
--- a/packages/cli/src/environments.ee/source-control/__tests__/source-control-export.service.test.ts
+++ b/packages/cli/src/environments.ee/source-control/__tests__/source-control-export.service.test.ts
@@ -1,5 +1,6 @@
 import type { SourceControlledFile } from '@n8n/api-types';
 import type {
+	Folder,
 	FolderRepository,
 	Project,
 	ProjectRepository,
@@ -57,6 +58,7 @@ describe('SourceControlExportService', () => {
 	);
 
 	const fsWriteFile = jest.spyOn(fsp, 'writeFile');
+	const fsReadFile = jest.spyOn(fsp, 'readFile');
 
 	beforeEach(() => jest.clearAllMocks());
 
@@ -273,6 +275,63 @@ describe('SourceControlExportService', () => {
 			expect(result.count).toBe(0);
 			expect(result.files).toHaveLength(0);
 		});
+
+		it('should not duplicate folders on push', async () => {
+			// Arrange
+			const newFolders = [
+				{
+					id: 'folder-id',
+					name: 'Folder Name',
+					parentFolderId: null,
+					homeProject: { id: 'project-id' },
+					createdAt: new Date(),
+					updatedAt: new Date(),
+				} as Folder,
+			];
+			folderRepository.find.mockResolvedValue(newFolders);
+			workflowRepository.find.mockResolvedValue([mock()]);
+			const existingFolders = [
+				{
+					id: 'folder-id',
+					name: 'Folder Name',
+					parentFolderId: null,
+					homeProjectId: 'project-id',
+					createdAt: new Date().toISOString(),
+					updatedAt: new Date().toISOString(),
+				},
+			];
+			fsReadFile.mockResolvedValue(
+				JSON.stringify({
+					folders: existingFolders,
+				}),
+			);
+
+			// Act
+			const result = await service.exportFoldersToWorkFolder(globalAdminContext);
+
+			// Assert
+			// new json file should contain only the new folders
+			expect(fsWriteFile).toHaveBeenCalledWith(
+				'/mock/n8n/git/folders.json',
+				JSON.stringify(
+					{
+						folders: newFolders.map((f) => ({
+							id: f.id,
+							name: f.name,
+							parentFolderId: f.parentFolderId,
+							homeProjectId: f.homeProject.id,
+							createdAt: f.createdAt.toISOString(),
+							updatedAt: f.updatedAt.toISOString(),
+						})),
+					},
+					null,
+					2,
+				),
+			);
+
+			expect(result.count).toBe(1);
+			expect(result.files).toHaveLength(1);
+		});
 	});
 
 	describe('exportVariablesToWorkFolder', () => {
diff --git a/packages/cli/src/environments.ee/source-control/source-control-export.service.ee.ts b/packages/cli/src/environments.ee/source-control/source-control-export.service.ee.ts
index 77d9ec98d88..6c0000398ea 100644
--- a/packages/cli/src/environments.ee/source-control/source-control-export.service.ee.ts
+++ b/packages/cli/src/environments.ee/source-control/source-control-export.service.ee.ts
@@ -20,7 +20,6 @@ import { UnexpectedError, type ICredentialDataDecryptedObject } from 'n8n-workfl
 import { rm as fsRm, writeFile as fsWriteFile } from 'node:fs/promises';
 import path from 'path';
 
-import { VariablesService } from '../variables/variables.service.ee';
 import {
 	SOURCE_CONTROL_CREDENTIAL_EXPORT_FOLDER,
 	SOURCE_CONTROL_GIT_FOLDER,
@@ -40,14 +39,15 @@ import {
 	stringContainsExpression,
 } from './source-control-helper.ee';
 import { SourceControlScopedService } from './source-control-scoped.service';
+import { VariablesService } from '../variables/variables.service.ee';
 import type { ExportResult } from './types/export-result';
 import type { ExportableCredential } from './types/exportable-credential';
+import { ExportableProject } from './types/exportable-project';
 import type { ExportableWorkflow } from './types/exportable-workflow';
 import type { RemoteResourceOwner } from './types/resource-owner';
 import type { SourceControlContext } from './types/source-control-context';
 
 import { formatWorkflow } from '@/workflows/workflow.formatter';
-import { ExportableProject } from './types/exportable-project';
 
 @Service()
 export class SourceControlExportService {
@@ -269,7 +269,7 @@ export class SourceControlExportService {
 			// keep all folders that are not accessible by the current user
 			// if allowedProjects is undefined, all folders are accessible by the current user
 			const foldersToKeepUnchanged = context.hasAccessToAllProjects()
-				? existingFolders.folders
+				? []
 				: existingFolders.folders.filter((folder) => {
 						return !allowedProjects.some((project) => project.id === folder.homeProjectId);
 					});