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OneDrive File Issues

How to Keep Desktop and Folder Files Separate Between Computers in OneDrive

Maira MehtabMaira Mehtab Sep 21, 2026 869 views

Question details

The user wants to prevent OneDrive from merging local folders across an old desktop and a new laptop so each device maintains its own separate files.

Product
OneDrive
Device & OS
not provided
Scenario
Setting up a new laptop with an existing OneDrive account where local folders are automatically syncing.
Observed behavior
Files from an old desktop computer and a newer laptop are automatically merged into the same directories after OneDrive folder backup is enabled on the new device.
Before you start

Before changing your OneDrive backup settings, ensure that all currently syncing files are fully uploaded to the cloud to prevent accidental data loss when unlinking local folders.

Solution 1Recommended

Disable Folder Backup in OneDrive Settings

Turn off the PC folder backup for specific folders like Desktop or Pictures on each computer to prevent them from merging across devices.

By default, OneDrive's PC folder backup feature synchronizes your Desktop, Documents, and Pictures folders to the cloud. When you sign in to a second computer with the same account, it merges the files. Disabling this feature locally keeps your computer's folders isolated.

1
Open OneDrive Settings

Click on the OneDrive cloud icon located in the Windows taskbar notification area, click the gear icon (Help & Settings), and select 'Settings' from the menu.

2
Navigate to Manage Backup

In the Settings window, go to the 'Sync and backup' tab and click on the 'Manage backup' button.

3
Disable Unwanted Folders

Toggle off the switches for the folders (such as Desktop, Documents, or Pictures) that you want to keep separate on this specific computer, then confirm your choice to stop backing up.

Minimum Folder Requirement: OneDrive may require at least one folder to remain selected for backup. Any folder you leave enabled will continue to synchronize across all connected devices.
Free Microsoft Office alternative

Looking for a More Flexible Document Storage Solution?

If OneDrive's aggressive folder merging is frustrating, consider switching to WPS Office. It offers an independent, stable cloud storage solution (WPS Cloud) that lets you easily manage document syncing without forcefully merging your computer's local Desktop folders.

  1. 1. Download and Install: Visit the official WPS website to download and install the free WPS Office suite on your computer.
  2. 2. Sign In to WPS Cloud: Open the application, create a free account, and sign in to access your dedicated WPS Cloud space.
  3. 3. Save Files Selectively: Save your documents directly to WPS Cloud only when you want them accessible on other devices, keeping your local Desktop clean.
Fully compatible with Microsoft Word, Excel, and PowerPoint formats (.docx, .xlsx, .pptx).Provides free WPS Cloud storage for easy, manual document syncing when you want it.Lightweight installation that does not interfere with your system's default local folders.All-in-one suite combining documents, spreadsheets, and presentations in a single interface.
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Frequently Asked Questions

Where do my files go after I stop OneDrive folder backup?

When you stop backing up a folder, the files that were already backed up remain in your OneDrive folder online. Your actual computer's Desktop or Documents folder may appear empty; you will see a shortcut titled 'Where are my files?' which you can use to drag them back to your local folder.

Can I use two different personal OneDrive accounts on the same computer?

No, Microsoft only allows you to link one personal OneDrive account and one business/school account on the same device. You cannot link two personal accounts simultaneously to keep files separate.

Why did my Desktop files suddenly merge onto my new laptop?

During the initial Windows setup or OneDrive installation on your new laptop, the 'PC folder backup' feature was likely enabled by default. This causes OneDrive to automatically download and merge your old desktop files onto the new computer's Desktop.