How to safely migrate from Exchange 2013 to Exchange Server SE in a production environmen

Hi @Colotta Jerrae

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

We understand you are looking for guidance on migrating from Exchange 2013 to Exchange Server Subscription Edition (SE). 

For safe migration plan  

As my research Exchange SE cannot coexist with Exchange 2013. This means you must move from Exchange 2013 to Exchange 2019, which supports coexistence, and then upgrade in place from Exchange 2019 CU14 or CU15 to SE. This approach is low-risk and similar to a cumulative update process.  

For your large environments, you could use Exchange 2019 as the coexistence bridge while migrating mailboxes, public folders, transport rules, connectors, and relay dependencies. Only after fully removing Exchange 2013 should you proceed to SE, as SE setup will block if 2013 servers are detected. 

Exchange 2019 and SE support Outlook 2013 and later, so your mix of Outlook 2016 and Microsoft 365 clients is fine. Validate older clients or EAS devices and deprecate legacy protocols/TLS versions before cutover. Inventory all Receive/Send connectors, permitted IP ranges, and TLS configurations early, and replicate these on Exchange 2019 and SE to maintain uninterrupted application relay. Microsoft recommends hardening SMTP and client protocols to TLS 1.2 or 1.3. 

If you retain public folders on-premises, migrate them to Exchange 2019 within the same forest and validate hierarchy and quotas before upgrading to SE. For hybrid environments planning cloud public folders, follow Microsoft’s batch migration guidance and size limits. 

SE uses a subscription licensing model. In-place upgrades from Exchange 2019 CU14 or CU15 to SE initially run with existing keys, but future SE cumulative updates will require SE product keys or qualifying licensing and Software Assurance. Plan your budget and entitlement accordingly. Maintain operational hygiene by following Microsoft’s deployment prerequisites, validating Active Directory health, and ensuring servers are at the latest CU and SU levels before any upgrade to reduce installation blockers and security risks. 

For handles hybrid configuration 

Microsoft recommends using the newest supported on-premises version as the hybrid anchor. Move hybrid to Exchange 2019 during the 2013 to 2019 phase, then upgrade those hybrid servers to SE. Continue using the Hybrid Configuration Wizard (HCW) to validate prerequisites and configure mail flow, OAuth, organizational relationships, and migration endpoints, always running the latest HCW build. 

Microsoft has introduced enforcement around the Dedicated Exchange Hybrid App in Entra ID and updated HCW accordingly, so ensure your tenant and hybrid servers comply to avoid disruptions such as free/busy or MailTips during enforcement windows. If you have fully moved user mailboxes to Exchange Online but keep an on-premises server for recipient management and SMTP relay, Microsoft’s hybrid license remains available, but staying eligible for SE updates aligns with subscription or Software Assurance requirements. 

For SMTP relay in hybrid scenarios, you can keep Exchange 2019 or SE as your internal relay host for applications and devices using locked-down Frontend Receive connectors. If relaying through Exchange Online, note the updated requirements: the certificate or MAIL FROM domain must match an accepted domain tied to an OnPremises connector, as the older “From header” match no longer qualifies. Customers decommissioning on-premises SMTP can consider dedicated SMTP servers or authenticated SMTP in Exchange Online, planning carefully for device and application support. 

Public folders can remain on-premises with Exchange 2019 or SE, or migrate to Exchange Online using Microsoft’s batch method, ensuring limits and staging plans to avoid user impact. Outlook autodiscover and cross-version proxying maintain continuity across Exchange 2013 to 2019 coexistence and into SE, provided namespaces and certificates remain consistent and all involved servers run the latest cumulative updates. 

For more details, you could refer to these references: 

Upgrading to Exchange Server Subscription Edition (SE) | Microsoft Learn 

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

Migrate public folders from Exchange 2013 to Exchange 2016 or Exchange 2019 | Microsoft Learn 

Hybrid deployment prerequisites | Microsoft Learn 

Hybrid Configuration wizard | Microsoft Learn 

I hope this helps address your concern. Please let me know if I misunderstood your request, and feel free to share any additional questions or comments. I’ll be more than happy to assist further. 

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