SharePoint Document Issues

How to Find Out Why SharePoint Deletes Empty Folders

Maira Mehtab Sep 30, 2026 870 views

Question details

Users need to determine the cause of SharePoint automatically removing empty folders that are created or synced for future use.

How to Find Out Why SharePoint Deletes Empty Folders

Product: Microsoft SharePoint
Device & OS: not provided
Scenario: Uploading or synchronizing empty folder structures for future document management.
Observed behavior: SharePoint automatically deletes the empty folders shortly after they are uploaded or synchronized, disrupting intended folder structures.

Before you start

Ensure you have tenant administrator privileges or coordinate with your IT department, as investigating this issue requires access to the Microsoft Purview compliance portal.

Solution 1Recommended

Investigate Deletions using Microsoft Purview

Use the Microsoft Purview audit logs to track deletion events and verify if automated retention policies are clearing empty directories.

In Microsoft 365 environments, unexpected folder deletions are often caused by automated retention policies, compliance rules, or background synchronization processes. By checking the audit logs, administrators can pinpoint exactly what system process or user account triggered the removal.

Access Microsoft Purview

Ask your tenant administrator or IT team to log in to the Microsoft Purview compliance portal using their administrator credentials.

Search the Audit Log

Navigate to the 'Audit' section from the left-hand menu. Search for folder deletion activities within the specific timeframe the folders disappeared to identify the exact user, sync client, or system process responsible.

Check Retention Policies

Go to the 'Data Lifecycle Management' or 'Records Management' section in Purview. Review active retention policies to determine if an automated rule is configured to delete empty or inactive folders across SharePoint sites.

Investigate Deletions using Microsoft Purview

Pro Tip: If the audit log doesn't show a deletion event, the issue might be caused by the OneDrive Sync client simply ignoring empty folders during upload rather than deleting them.

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Frequently Asked Questions

Why does the sync client ignore my empty folders in SharePoint?

Synchronization tools like the OneDrive sync client are often designed to skip empty folders during the sync process to save bandwidth and prevent clutter. This makes the folders appear as if they were deleted on the cloud side, even though they simply weren't uploaded.

Can I recover empty folders deleted by SharePoint policies?

Yes, if the folders were actually deleted (and not just skipped during sync), they can typically be restored from the SharePoint Site Recycle Bin within 93 days of the deletion event.

How can I prevent SharePoint or sync clients from removing my empty folders?

You can place a small placeholder file, such as a blank text document (.txt), inside the folder. This ensures the folder is no longer empty, forcing the sync client to upload it and protecting it from empty-folder cleanup policies.

Who has permission to view the Microsoft Purview audit logs?

Only users assigned specific administrative roles in Microsoft 365, such as Global Administrator, Compliance Administrator, or Audit Manager, have the necessary permissions to access and search the audit logs in Microsoft Purview.

Document & File Issues