How to migrate user mailboxes in an Exchange hybrid setup

Hi @Rachal Camp

Thank you for posting your question in Microsoft Q&A. 

I understand that you are considering migrating user mailboxes in your hybrid tenant using a recommended and stable approach. 

For ensuring minimal downtime and no mail flow disruption 

You could use the "manual complete" option in batches, this syncs 95% of data in the background while the user accesses the on-premises mailbox. Incremental syncs occur every 24 hours. Finalization (the last 5%) takes minutes (typically under 10) during a maintenance window. Users may experience brief Outlook disconnects, but OWA/OWA offline mode remains accessible. 

With mail flow: In hybrid, mail routing uses targetAddress attributes updated automatically post-move. Inbound mail routes via on-premises (if MX points there) or directly to EXO. Outbound uses hybrid connectors. During sync, all new mail delivers to the on-premises mailbox and syncs over. No rerouting needed until finalization, and hybrid ensures unified GAL for seamless sending/receiving. 

To ensure, you could schedule finalization off-hours, notify users, and monitor with Get-MoveRequestStatistics. Avoid peak times to prevent network saturation. 

For recommend steps 

As my research, before initiating mailbox migrations, ensure the following prerequisites are in place: 

1.Hybrid Configuration: A fully configured hybrid deployment between your on-premises Exchange Server and Exchange Online, set up using the Hybrid Configuration Wizard (HCW). This enables seamless connectivity, directory synchronization via Microsoft Entra Connect (formerly Azure AD Connect), and features like free/busy sharing. 

2.MRSProxy Service: Enable the Mailbox Replication Proxy (MRSProxy) on all on-premises Exchange Client Access Servers (CAS) or Edge Transport servers.  

3.Permissions: The admin account performing the migration must have the "Mailbox Move" role or be part of the Organization Management group in both on-premises and Exchange Online. Use RBAC (Role-Based Access Control) to assign these. 

4.Licenses: Assign an appropriate Microsoft 365 license to the user in Exchange Online, but only after the migration completes (you have up to 30 days post-move). 

5.Directory Sync: Users must be synced to Microsoft Entra ID with matching attributes. For shared mailboxes, ensure they're mail-enabled users in on-premises AD and synced. 

6.Network and Firewall: Open ports for MRS (TCP 443 for HTTPS) and ensure stable connectivity to Exchange Online endpoints. Test with tools like the Microsoft Remote Connectivity Analyzer. 

Initiating Remote Move Migrations 

Remote move migrations use the Mailbox Replication Service (MRS) to move mailboxes with synchronization, allowing for batched operations.  

You can use the Exchange Admin Center (EAC) for a GUI approach or PowerShell for scripting/automation. Focus on batches of 50-100 mailboxes to manage load. 

1.Using Exchange Admin Center (EAC) 

Navigate to Recipients > Migration. 

Select Migrate to Exchange Online > Remote move migration. 

Add users (individually or via CSV for large batches). 

Create or select migration endpoint (pointing to on-prem EWS URL). 

Configure settings: target delivery domain, bad item limit. 

Schedule batch: choose Manually complete later for minimal downtime. 

Start batch and monitor status. 

Note: Remove the batch after completion to avoid conflicts in future moves.  

2.Using PowerShell 

Connect to Exchange Online 

Run 

New-MigrationEndpoint

To create the endpoint if needed. 

New-MigrationBatch -Name "Batch1" -SourceEndpoint $endpoint.Identity -CSVData (Get-Content "users.csv" -Encoding Byte) -TargetDeliveryDomain "domain.com" -AutoComplete $false
Start-MigrationBatch -Identity "Batch1"
Get-MigrationBatch / Get-MigrationUserStatistics
Complete-MigrationBatch -Identity "Batch1"

You can test with a pilot batch of 5-10 users.

Estimated setup time: 10-15 minutes per batch, but actual move depends on size/network.

For Handling Large Mailboxes  

Large mailboxes (for example, over 50GB primary, or with archives over 100GB) require pre-migration optimization to avoid timeouts, throttling, or failures.

Exchange Online limits: Primary up to 100GB (standard), archives unlimited with auto-expanding enabled. 

1.Pre-Migration Preparation: 

Enable auto-expanding archives in Exchange Online:

Set-OrganizationConfig -AutoExpandingArchive. 

Provision cloud archives for users via PowerShell:

Enable-RemoteMailbox -Identity ******@domain.com -RemoteArchive. 

Use retention policies to move older items from primary to archive: Create a policy in on-premises EAC (Compliance Management > Retention Policies) to tag items >X days and move to archive. Apply to mailboxes and run Start-ManagedFolderAssistant to process. 

For mailboxes >100GB primary or >240GB archive: Reduce primary size below 100GB by moving content to cloud archive first. Split oversized data (>1.5TB total) across multiple mailboxes. 

Tune on-premises Managed Folder Assistant: Set registry key for higher item processing limits (such as 10,000 items per cycle) and restart services. 

2.During Migration: 

Migrate archives first if separate, then primary. Use batching and monitor MRS performance. Increase MRS workers on on-premises servers if needed (via config files). 

Handle throttling: Follow Microsoft 365 migration performance guidelines, migrate during off-peak hours, ensure high-bandwidth connections (at least 100Mbps), and use multiple endpoints if available. 

You should focus on: 

Aim for primary <100GB before final move. 

Preserve legal holds: Sync holds to cloud and enable on target objects. 

For recoverable items, set policies to move only older than deleted-item retention period. 

If >240GB archive, use third-party tools or manual export/import as fallback (not recommended for hybrid). 

This approach can reduce migration time from days to hours. 

You could refer to: Migrate large mailboxes from on-premises Exchange to Microsoft 365 Exchange | Microsoft Learn 

For ensuring Outlook, Mobile Clients, and Delegated Access  

Outlook: Autodiscover updates automatically, restart Outlook post-move. Enable Hybrid Modern Authentication for smoother transitions. 

Mobile Clients: Autodiscover redirects to Exchange Online, may require re-authentication. Update apps if needed. 

Delegated Access: Permissions sync in hybrid. Move delegators and delegates together. Verify with this command: 

Get-MailboxPermission 

I have found some relevant Microsoft articles that may help. You can refer to them here: 

Move mailboxes between on-premises and Exchange Online organizations in hybrid deployments | Micros… 

Performance factors and best practices for hybrid migrations | Microsoft Learn 

Outlook cannot connect or web services cannot work after migrated to Microsoft 365 - Outlook | Micr… 

If you have any additional concerns, feel free to comment below. I would be more than happy to assist. 

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