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Email Migration

Fix Microsoft 365 Migration from Exchange 2016 Failing Issue

Khadija KhanKhadija Khan Sep 27, 2026 869 views

Question details

Users are experiencing recurring failures when attempting to migrate mailboxes from an on-premises Exchange 2016 environment to Microsoft 365.

How to Fix Microsoft 365 Migration from Exchange 2016 Failing
Product
Microsoft Exchange 2016 and Microsoft 365
Device & OS
not provided
Scenario
Migrating on-premises Exchange 2016 mailboxes to the Microsoft 365 cloud infrastructure.
Observed behavior
The email migration process fails repeatedly, often due to underlying issues with administrative permissions, Autodiscover, Outlook Anywhere endpoints, or Azure AD synchronization dependencies.
Before you start

Ensure you have Global Administrator privileges in your Microsoft 365 tenant and Organization Management permissions in your on-premises Exchange 2016 environment before making any configuration changes.

Solution 1Recommended

Validate Migration Endpoints and Permissions

Verify that your migration endpoints, MRS Proxy, and administrative permissions are correctly configured to establish a secure connection between on-premises and cloud servers.

A successful mailbox move requires a flawless connection between Microsoft 365 and your local Exchange server. If the Mailbox Replication Service (MRS) Proxy is disabled or your endpoint certificates are invalid, the migration batches will fail immediately.

1
Enable the MRS Proxy Endpoint

Open the Exchange Admin Center (EAC) on your Exchange 2016 server. Navigate to Servers > Virtual Directories, select the EWS (Default Web Site) directory, click the Edit icon, and ensure the 'Enable MRS Proxy endpoint' checkbox is selected.

2
Test Autodiscover and Outlook Anywhere

Use the Microsoft Remote Connectivity Analyzer tool online. Run tests for Outlook Anywhere and Autodiscover to ensure external Microsoft 365 services can securely discover and connect to your local server.

3
Verify Administrator Roles

Ensure the administrator account used for the migration has the 'ApplicationImpersonation' role assigned and possesses 'Receive As' permissions on the targeted Exchange mailbox databases.

4
Validate Endpoint in Microsoft 365

Log into the Microsoft 365 Admin Center, navigate to Show All > Exchange, select Migration, and click on Endpoints. Test the existing Exchange 2016 endpoint to confirm a successful connection.

Validate Migration Endpoints and Permissions
Apply Changes via IIS Reset: If you just enabled the MRS Proxy, open a Command Prompt as administrator and run 'iisreset' to ensure the changes take effect immediately across your Exchange services.
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Frequently Asked Questions

Why does a cutover migration fail when Active Directory synchronization is enabled?

Cutover migrations are designed for environments where directory synchronization is not used. If Azure AD Connect is already synchronizing accounts and Microsoft 365 mailboxes exist, the cutover batch will fail due to duplicate object conflicts. A hybrid migration should be used instead.

What is the MRS Proxy, and why is it needed for Exchange 2016 migration?

The Mailbox Replication Service (MRS) Proxy is an Exchange server component that facilitates cross-forest mailbox moves. It must be enabled on the Exchange 2016 EWS virtual directory to allow Microsoft 365 to securely pull mailbox data from your on-premises servers.

How do I view detailed error messages for my failed migration batches?

You can view detailed logs in the Microsoft 365 Admin Center. Navigate to the Exchange Admin Center, select Migration, click on the failed migration batch, and select 'View details' on the right pane to see specific error codes and failure reasons for individual mailboxes.

Do I need to reconfigure Outlook Anywhere for a Microsoft 365 migration?

Yes, your migration endpoints rely heavily on Outlook Anywhere (RPC over HTTP) or MAPI over HTTP to connect securely. If your SSL certificates are invalid or external URLs are configured incorrectly, the connection to Microsoft 365 will fail.