SharePoint migration manager File Share agent to migrate local drive did not preserve the permissions

Create a folder inside the destination document library and migrate the file-share root into that folder, because Migration Manager does not migrate source root-folder permissions when the document library itself is selected as the destination.^1^

Correct the migration

1. In the destination SharePoint document library, create a new folder, such as MigratedData.
2. In SharePoint admin center → Migration → Migration Manager, create a new migration task.
3. Select the same local/file-share source.
4. For the destination, select the newly created MigratedData folder—not the document library root.
5. Keep Preserve file share permissions enabled.
6. Under the task’s user settings, use either:
   • Microsoft Entra lookup, which maps source identities automatically; or
   • A user mapping file for identities that cannot be resolved automatically.^2^
7. Run a pilot and inspect Manage Access on the new destination folder and representative child folders before migrating the remaining data.

An existing task cannot be redirected to a different destination after its initial migration, so addressing the library-root exception requires a new task.^3^

After validating the new copy, either direct users to it or move it into the intended information architecture. Avoid deleting the existing copy until permissions and content have been compared.

Verify which source permissions are eligible

The setting does not preserve every kind of Windows permission:

• Users and groups must be synchronized or otherwise mapped to Microsoft Entra ID.
• Only NTFS permissions exposed through Windows File Explorer—or NTFS-equivalent permissions exposed over SMB—are migrated.
• Permissions granted only at the share level are not migrated.
• Advanced NTFS permissions, auditing settings, and explicit deny entries are not preserved.
• The most restrictive applicable share or NTFS permission determines the resulting SharePoint access level.^4^^5^

Before rerunning, check the source folder’s Properties → Security tab—not only Properties → Sharing. Confirm that every required source user and group has a corresponding Microsoft Entra identity. Unresolved identities can leave migrated content without the expected role assignments.

Repair content already migrated

A normal delta sync will not necessarily repair permissions by itself. Migration Manager updates permissions during delta sync only when the corresponding file is transferred. A permission-only source change does not alter the file’s modified timestamp, so the default incremental mode may skip it.^3^

For child content whose destination is otherwise correct:

1. Open the task’s Project settings → Advanced.
2. Set file-transfer behavior to Migrate all files and overwrite any existing ones at the destination.
3. Run delta sync.
4. Recheck representative folder and file permissions.

This is slower and overwrites destination files, including destination-side content changes, so preserve or reconcile any changes users made after migration. It also does not overcome the document-library-root exception; use the new-folder/new-task approach for that issue.

The screenshot states that the folder inherits from its parent. Therefore, its effective access is determined by the parent even though the current folder’s permissions view lists no direct assignments. Use Check Permissions for a representative user to verify effective access rather than relying only on the empty list.

References

1. Permission settings in Migration Manager
2. Migration Manager Settings
3. Delta Sync
4. Data Migration
5. Guide to migrating file shares to OneDrive, Teams, and SharePoint