SharePoint Document Issues

How to Fix SharePoint Creating a Second Company Folder in File Explorer

Jason MillerJason Miller Oct 23, 2026 869 views

Question details

The user wants to consolidate synchronized SharePoint sites because synchronizing document libraries is creating a duplicate company-named folder in File Explorer.

How to Fix SharePoint Creating a Second Company Folder in File Explorer
Product
SharePoint
Device & OS
Windows 10
Scenario
Synchronizing SharePoint document libraries to a local computer via the OneDrive sync client.
Observed behavior
A second, duplicate company folder is created in Windows 10 File Explorer instead of grouping all synchronized sites under the single original organization folder.
Before you start

Before making changes to your synchronization settings, ensure you do not manually delete any folders from File Explorer while they are still syncing, as this will permanently delete the files from the SharePoint cloud for all users.

Solution 1Recommended

Unlink and Re-synchronize the SharePoint Library

Identify the duplicate synchronization connection and unlink it via OneDrive settings to consolidate your synchronized folders.

When you click Sync on a SharePoint site, the OneDrive client typically synchronizes the library under your main organization name. A second folder usually indicates an additional OneDrive account connection, a separate organization connection, or a temporary synchronization glitch.

1
Open OneDrive Settings

Right-click the blue OneDrive cloud icon located in the Windows 10 taskbar notification area (system tray) and select the Settings (gear) icon.

2
Locate the problematic sync

Navigate to the 'Account' tab. Look at the list of all currently synchronized locations to identify the SharePoint library that corresponds to the duplicate company folder.

3
Stop syncing the library

Click the 'Stop sync' button next to the problematic SharePoint library and confirm your choice. The local folder will stop receiving updates.

4
Remove the duplicate local folder

Open File Explorer and safely delete the now-unlinked duplicate local folder. Make sure the green sync checkmark is completely gone before deleting to ensure cloud files are safe.

5
Re-synchronize from SharePoint

Return to the correct SharePoint document library in your web browser, ensure you are logged into the correct Microsoft 365 account, and click the 'Sync' button to re-establish the connection under the proper root folder.

Unlink and Re-synchronize the SharePoint Library
Verify with colleagues: Check whether your colleagues are experiencing the same duplicate folder issue. If they are, the problem might be related to how the SharePoint site name or tenant organization profile was recently configured by your IT administrator.
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  1. 1. Download WPS Office: Visit the official WPS website and download the free WPS Office installer for Windows.
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  3. 3. Enable WPS Cloud: Sign in with a free account to activate WPS Cloud, allowing you to easily save and sync files without creating duplicate folders in File Explorer.
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Frequently Asked Questions

Why does OneDrive create a completely separate folder for my SharePoint sync?

Typically, OneDrive groups all SharePoint syncs under a single organization name (e.g., 'Contoso'). A separate folder might be created if the site belongs to a different Microsoft 365 tenant, if you signed into a secondary account, or if a temporary sync error forced OneDrive to create a duplicate folder to avoid file conflicts.

Is it safe to delete the duplicate company folder from File Explorer?

Do not delete the folder while it is still actively syncing, as this action will delete the files for everyone in the SharePoint cloud. You must stop the sync from your OneDrive settings first, verify the sync status icon is gone, and only then remove the local folder.

Can I manually rename the company folder created by SharePoint in File Explorer?

No, you cannot manually rename the root organization folder created by the OneDrive sync client in Windows File Explorer. The folder name is automatically generated and dictated by your organization's Microsoft 365 tenant profile.

How do I force all my SharePoint sites to group into one folder?

You cannot manually drag and drop them into a single folder. You must ensure all sites are synced using the exact same Microsoft 365 user account. If they are split erroneously, stopping the sync for the detached sites and re-syncing them typically forces OneDrive to place them into the correct main organization folder.