Guidance needed for migrating from Exchange 2016 to Exchange Server SE

Question

I’m planning to migrate our on-premises environment from Exchange Server 2016 to Exchange Server SE, and I’m trying to understand the correct upgrade/migration path. Since SE is subscription-based and not a typical cumulative update, I’m unsure whether the process is closer to an in-place upgrade or a full side-by-side migration.

Specifically, I’m looking for guidance on:

• Recommended migration steps from 2016 to SE
• Whether a coexistence period is required
• Any schema updates or prerequisite changes
• Mailbox move considerations and downtime expectations
• Known limitations or blockers when transitioning from 2016 to SE

Has anyone done this migration or can point me to the right approach and best practices?

Answer 1

Hi @Santiago Cruz

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

We understand that you are considering a migration plan from Exchange Server 2016 to Exchange Server Subscription Edition (SE). 

For your concerns: 

Recommended Migration Steps 

The recommended path for migrating from Exchange Server 2016 to Exchange Server Subscription Edition (SE) is a legacy upgrade (side-by-side migration), as direct in-place upgrades are not supported from 2016. This involves deploying new SE servers alongside your existing 2016 environment, migrating resources, and decommissioning the old servers. An alternative is to first legacy upgrade to Exchange 2019 CU15, then perform an in-place upgrade to SE. 

Alternative step: You could consider to first perform a legacy upgrade to Exchange Server 2019 CU15, and then proceed with an in-place upgrade from Exchange 2019 to Exchange SE. 

You can refer via: Upgrading to Exchange Server Subscription Edition (SE) | Microsoft Learn 

For Coexistence Period: 

As my research, a coexistence period is required and supported during the migration. Exchange Server SE RTM and CU1 can coexist with Exchange 2016 (up to CU23) and 2019 in the same organization, allowing gradual mailbox moves without immediate disruption. However: 

Coexistence is not supported long-term. Starting with SE CU2 (expected in late 2025 or early 2026), installation will block any unsupported versions (including 2016 and pre-CU14 2019). You must fully decommission 2016 servers before upgrading to CU2. 

A direct  migration (all at once) is risky for most organizations due to potential downtime, testing needs, and scale (for example, thousands of mailboxes). Coexistence lets you phase the process over weeks or months, minimizing user impact. 

Schema updates or prerequisite changes 

Schema Updates: As part of the legacy upgrade, the Active Directory (AD) schema must be extended to the SE level. This process occurs automatically during SE setup when run with elevated privileges using: Setup.exe /PrepareSchema /IAcceptExchangeServerLicenseTerms. Run this command from the SE installation media on a domain controller or schema master. No additional manual schema changes are required, but ensure you back up AD beforehand. The schema version for SE aligns with Exchange Server 2019. 

Prerequisites: 

Software Requirements: Exchange 2019 and SE share the same prerequisites, including: 

.NET Framework, Unified Communications Managed API (UCMA), Visual C++ Redistributables, Required Windows Features, Supported Operating System: Windows Server 2022, Active Directory Requirements: Forest and domain functional levels: Windows Server 2016 or higher recommended 

Server Roles and Editions: No changes to roles or editions (Standard/Enterprise) 

Security: Ensure all servers have the latest security updates installed. 

You can refer more via:  

Prepare Active Directory and domains for Exchange Server, Active Directory Exchange Server, Exchang… 

Exchange Server 2019 and SE system requirements— memory requirements and client compatibility | Mic… 

Mailbox move approachs and Downtime expectations  

If both Exchange servers are in coexistence and fully configured, begin by creating a test mailbox on the new Exchange server and connect it using Microsoft Outlook. Verify email delivery and access before migrating live data. Once validated, use the PowerShell command New-MoveRequest to move mailboxes from Exchange Server 2016 to the new server. This command supports online intra-org moves via the Mailbox Replication Service (MRS).

Start with arbitration/system mailboxes, then batch user mailboxes (50–100 at a time) by size or department to avoid overload.

Moves support mailboxes up to 100GB,monitor progress with Get-MoveRequestStatistics.

In DAG environments, maintain high availability during moves.

Public folders require separate migration scripts.

Downtime is minimal (seconds-minutes per mailbox for final sync/cutover), users stay connected to source during sync. Full org migration (500-2000 mailboxes) takes arround 2-4 weeks. No user impact if using cached Outlook mode; schedule batches off-hours for large moves. 

You can refer via: Migrate Exchange 2016 to Exchange Server SE - Complete Guide 

Note: Microsoft is providing this information as a convenience to you. These sites are not controlled by Microsoft, and Microsoft cannot make any representations regarding the quality, safety, or suitability of any software or information found there. Please ensure that you fully understand the risks before using any suggestions from the above link. 

Known limitations or blockers when migrating from 2016 to SE 

As noted earlier, there is no direct in-place upgrade path from Exchange 2016, migration is mandatory. Installing SE CU2 will block further coexistence with Exchange 2016, requiring migration to be completed. Exchange 2016 reached end of support (EOS) on October 14, 2025, no additional cumulative updates or security patches will be released beyond the optional six-month ESU period. Please migrate promptly to mitigate security and operational risks. 

Licensing: Exchange SE requires an active subscription. Traditional perpetual licenses will not remain valid post-EOS unless covered by Software Assurance. 

Coexistence Risks: After CU1, coexistence is unsupported. This may lead to issues with features such as free/busy calendar sharing or cross-version DAG maintenance. 

You could refer more via:  

Upgrading your organization from current versions to Exchange Server SE | Microsoft Community Hub 

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

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