Microsoft 365 Migration

Fix Missing Customizations After SharePoint 2013 to SharePoint Online Migration

Olivia MillerOlivia Miller Oct 26, 2026 869 views

Question details

Users experience missing templates, navigation structures, and custom web parts after completing a migration from an on-premises SharePoint environment.

How to Fix Missing Customizations After Migrating to SharePoint Online
Product
SharePoint Online
Device & OS
not provided
Scenario
Migrating a large on-premises SharePoint 2013 site to Microsoft SharePoint Online using the SharePoint Migration Tool (SPMT).
Observed behavior
Customizations such as site templates, custom web parts, and specific navigation elements do not appear as expected in the destination environment.
Before you start

Ensure you have SharePoint Administrator privileges and access to the SharePoint Migration Tool (SPMT) logs to review specific migration errors and unsupported item reports.

Solution 1Recommended

Verify SPMT Supported Features and Enable Custom Scripts

Check which list templates and web parts are officially supported by the SharePoint Migration Tool and adjust admin settings to allow custom scripts.

Site-template migration heavily depends on the tool settings, enabled site features, and the destination environment. Not all SharePoint 2013 customizations are supported natively by SharePoint Online or the SPMT.

1
Review Supported Templates

Check the official Microsoft SPMT documentation to confirm if your specific SharePoint 2013 list templates and web parts are supported for direct migration.

2
Access SharePoint Admin Center

Log in to the Microsoft 365 admin center, navigate to the SharePoint admin center, and click on 'Settings' in the left-hand menu.

3
Enable Custom Scripting

Locate the 'Custom Script' setting and allow users to run custom scripts on personal sites and self-service created sites, which can help certain customizations render correctly.

Verify SPMT Supported Features and Enable Custom Scripts
Administrator Action Required: Changes to custom script settings in the SharePoint Admin Center may take up to 24 hours to take effect across your tenant.
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  1. 1. Download and Install: Download WPS Office from the official website and install it on your PC or Mac.
  2. 2. Open Migration Logs: Launch WPS Spreadsheet and open your SPMT migration CSV logs to audit missing files.
  3. 3. Analyze the Data: Use built-in filtering and formatting tools to quickly identify failed web part migrations and share the reports with your team.
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Frequently Asked Questions

Why are my custom web parts missing after using the SharePoint Migration Tool?

The SharePoint Migration Tool (SPMT) does not support all legacy customizations from SharePoint 2013. Highly customized web parts rely on outdated code structures and must be manually recreated using the modern SharePoint Framework (SPFx).

How do I enable custom scripts in SharePoint Online?

You can enable custom scripts by logging into the SharePoint Admin Center, navigating to Settings, selecting 'Classic settings page', and modifying the Custom Script settings to allow users to run custom scripts.

Does the SharePoint Migration Tool copy site navigation exactly as it was?

Navigation migration depends on the site template and tool settings. While structural navigation often migrates successfully, highly customized or managed metadata navigation may not appear as expected and will require manual reconfiguration in SharePoint Online.