Microsoft 365 Migration

Fix SharePoint Migration Manager Not Scanning Root Folder Files

Algirdas Jasaitis Sep 28, 2026 869 views

Question details

SharePoint Migration Manager successfully scans subfolders but completely skips files that are stored directly in the root of the file-share source path.

How to Fix Migration Manager Not Scanning Files in the Root Folder

Product: Microsoft 365 Migration Manager
Device & OS: not provided
Scenario: Migrating files from a local file share to Microsoft 365 using the Migration Manager tool.
Observed behavior: The system processes and migrates subfolder contents correctly, but misses any individual files located directly in the root directory.

Before you start

Ensure you have Microsoft 365 global admin or SharePoint admin permissions, and verify that the files in the root folder are not currently open or locked by another application.

Solution 1Recommended

Add the Root Directory as a Separate Source Path

Manually adding the root path separately forces the Migration Manager to scan and include the files located at the root level.

When you select the option to add all subfolders in Migration Manager, it often restricts its scan exclusively to those subdirectories. By explicitly defining the root folder as an independent source path, you bypass this limitation and guarantee that your root files are queued for migration.

Open Migration Manager

Add a New Task

Click on 'Add task' or select your existing file-share migration setup.

Specify the Root Path

Enter the UNC path of the root directory as a completely separate, standalone source path without relying on the 'create subfolder source paths' option.

Run the Scan

Save your configuration and manually initiate a new scan for this specific root path task.

Add the Root Directory as a Separate Source Path

Scan Delays: Sometimes the root folder files might appear in the scan results on the following day due to server-side processing delays, but adding the path manually remains the most reliable method.

Solution 2

Contact Microsoft Support for Server-Side Investigation

If manually adding the root path fails to resolve the issue, Microsoft support must investigate the backend activity logs.

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Frequently Asked Questions

Why does the 'create subfolder source paths' option ignore root files?

The current scanning logic for this specific feature is heavily optimized to parse subdirectories, which can occasionally cause the scanner to skip loose files stored at the absolute top-level root directory.

Do I need to wait 24 hours for the Migration Manager to find root files?

While some users report that root files are eventually discovered the following day due to delayed backend processing, adding the root directory as an explicit, separate source path provides an immediate fix.

Can this scanning failure cause data loss during migration?

Files skipped during the initial scan will not be migrated, meaning they are left behind on the original file share. Always review your post-migration summary reports to ensure no root files were missed.

Migration & Recovery