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Exchange 2016 to Exchange SE Migration​ Done Right

  Tej Pratap Shukla
Written By Tej Pratap Shukla
Anuraag Singh
Approved By Anuraag Singh
Modified On November 26th, 2025
Reading Time 6 Min Read

I recently assisted in an Exchange 2016 to Exchange SE migration, and I made some mistakes that you dont have to. Follow my guide in its entirety, and I promise the transfer you are dreading will be done in no time.

Table of Contents

Unfortunately, there is no in-place upgrade that allows you to directly move from already expired Exchange Server 2016 to the new and improved Subscription Edition. Instead, we have to follow a process similar to an Exchange 2016 to 2019 migration.

Don’t worry, my guide covers the entire lifecycle of this project: the pre-migration checklist, the “minefield” of manual migration, and the automated solution that bypasses the pain.

Let’s start with the prerequisites first.

Exchange 2016 to Exchange SE Pre-Migration Tasks

Check the latest official system requirements for the new server and make sure you have all the necessary hardware in pristine condition.

Like, for example, Exchange SE explicitly mentions the availability of at least 128 GB RAM, which is quite a huge jump considering the 2016 edition could work with just 8 GB of memory.

The oldest Windows Server you can use for SE is 2019, compared to the majority of the Exchange 2016 installations, which were on Windows Server 2012 to 2016.

Therefore, obtaining a new OS is a top priority for Exchange 2016 to Exchange SE Migration.

Any loose ends will cause the installation to falter, and you may even risk losing your data.

There is no overlap between what used to work for Exchange 2016 and what is necessary to run Exchange SE.

The Active Directory offers a bit more flexibility. You remain functional even on the Windows Server 2012 R2 (though 2016+ is recommended).

Make any other necessary updates to the schema (do it for each domain individually). Don’t forget to add the IIS Rewriter Module, the .NET 4.8.1, and Visual C++ 2012/2013 redistributables.

Ensure you export all (*.pfx) security certificates and private keys.

Special instructions for those operating a hardware load balancer (e.g., F5, Kemp, etc). Make a new pool for Exchange SE. Don’t cut over the existing VIP (Virtual IP), as it could jeopardize the transfer.

How to Migrate Exchange 2016 to Exchange SE Manually (and Why I Avoid It)?

There are two manual approaches. The first one involves the use of Exchange Admin Center (EAC), while the other uses PowerShell’s New-MoveRequest command.

If you try these methods in a lab environment with synthetic user data, it may seem super simple. However, in the real world, their actual limitations get exposed.

Failure at 95% prevents a Full Exchange 2016 to Exchange SE Migration​

Let’s consider a typical scenario: an admin like yourself prepares a batch of 50 users (typical for any small to medium-sized organization). He then starts a manual migration on Friday evening (smart decision, as during Weekends, regular use activity is slow, so more resources could be dedicated towards the migration)

However, when he comes back on Monday, assuming migration would be over by then and he could get the report, what he sees instead is that the batch is stuck at 95% synced.

Upon diagnosis, it is found that “Bad Items” (it could be corrupt calendar events or malformed MIME content) choked the migration pipeline. So the migration has to be postponed.

Data Transfer Stalls, and you can’t migrate Exchange 2016 to Exchange SE manually.

Exchange Server migration usually involves a terabyte of data. Now the problem is that you will be conducting the migration via the old hardware.

This could result in errors like mailboxes dismounting, extending the migration duration, and causing downtime for the users.

Lack of visibility and any real-time tracking is another reason why I won’t ever go with the manual method again. Then you might ask what the solution is. It’s simple, just use the most tried and tested solution.

Professional Exchange 2016 to Exchange SE Migration

The SysTools Exchange Migration Solution is simply the best. It offers transparent one-time pricing with a script-free GUI-style portal.

Download Now Purchase Now

Both small organizations and large enterprises love how simple and swift it is to move data between two different Exchange Servers with this tool at their disposal.

No matter what your reason to migrate is, this tool has you covered. Whether you want to adopt Exchange Server SE before your peers, or you dont want to deal with the security implications of both Exchange 2016 and Exchange 2019 EOL

You can try out the tool for free today. Simply download, install, and continue with the instructions below.

See How Easy it is to Load and Use the Tool

Here, I will explain the entire Exchange 2016 to Exchange SE Migration​ Step by Step via the automated tool:

Step 1: Get a copy of the software for your machine. On the setup screen, pick the correct endpoints, i.e., Exchange as both source and Destination.

SysTools Exchange 2016 to Exchange Server SE Migration tool set up page

Step 2: Select the exact workload you want to shift (Emails, Contacts, Calendars) and apply a timeline filter too.

filters to Migrate Exchange 2016 to Exchange Subscription Edition

Step 3: On the Source Screen, choose the correct Server configuration from the Dropdown and fill in all the mandatory details. Validate and hit Next. Repeat for the destination as well.

provide details

Step 4: Map the user from source to destination with the direct Fetch option or via the CSV Download – Import combo.

users list

Step 5: The Final step is to monitor the user list within the Tool’s UI, select the users, validate them, and then press Start. That’s it, the tool handles the rest on its own.

validate users and perform Exchange 2016 to Exchange SE migration

Post Migration Guidelines for Exchange 2016 to Exchange SE Migration​

Moving the data is the most important part, but your job isn’t done yet. Follow this guide to completely quit the old server safely.

  • Update the Firewall NAT rules to point towards the new server IP addresses.
  • Make changes to your DNS records so that OWA, the clients, and every other piece of infrastructure that you use are on the same page.
  • A smart tip that I, and many other veteran admins, follow is to lower DNS TTL (Time to Live) to 5 minutes.

Conclusion

Here, I showcased my strategy for the Exchange 2016 to Exchange SE migration. You have two options right now: either struggle with the manual bit-by-bit transfer or choose the right tool and migrate with ease.

With the tool, you transform a multi-week downtime-ridden project into a smooth, predictable, and fast process.