How to migrate from Exchange Server 2016/2019 to Microsoft 365

As you may already know, Exchange Server 2016 and 2019 have reached end of life and are no longer officially supported by Microsoft. If your organization still uses either of these platforms to manage email, contacts, calendars, and tasks, keep in mind that:

• Your environment may become vulnerable to newly discovered security threats – Microsoft will no longer provide security updates for Exchange 2016 and 2019 (unless you’ve enrolled in the Extended Security Update program, which ends in October 2026).
• Your emails may get blocked – Microsoft has started to throttle and block emails sent from unsupported Exchange Server versions to Exchange Online (as I covered in this article).

That said, migrating to a supported platform is now the only viable long-term option for keeping your organization’s email environment secure, supported, and fully operational.

If your organization wants or needs to keep things on‑premises (and continue using Microsoft’s solutions for that), upgrading to Exchange Server Subscription Edition (SE) is the only path forward. But given Microsoft’s clear preference for its cloud services – evident in the faster rollout of new features and the many security capabilities available exclusively in Microsoft 365 (Office 365) – now is a great time to leave your on‑prem environment behind and migrate to Exchange Online as part of Microsoft 365.

While switching over to a new platform might seem like a rough ride, I’ll show you some easy ways to follow when migrating mailboxes from Exchange Server 2016/2019 to Microsoft 365.

How to prepare for email migration to Microsoft 365

Before you start the migration process, you need to make sure your environment is ready for the move. For this purpose, you can use this guide in the Microsoft 365 admin center – it will help you connect your organization to Microsoft 365 and integrate your existing user accounts with Microsoft Entra ID.

Microsoft also recommends completing the steps below:

• Set up an SPF record to determine valid email sources for your organization’s Microsoft 365 domain.
• Set up the Exchange Online Protection service as a means of protection against spam and malware.
• If you’re behind on updates, make sure to install the latest Cumulative Update (CU).

And here is my quick, less obvious Microsoft 365 migration checklist:

• Verify if your software will work in Microsoft 365 (especially when it comes to server software). Microsoft 365 migration might be the time you learn that there is crucial legacy software that half the company uses and which is hard to replace.
• Encourage the whole company to clean up projects. It’s much easier to do this before the migration and start fresh.
• Gather as much information about your on‑premises environment as possible. For example, you might need to recreate access roles and permissions from scratch in the cloud or set up mail flow rules. Without prior research, it will be much more difficult.
• Verify if you need to migrate service accounts. There can be a lot of them on‑premises and in most cases, you won’t need them after the move.
• Review mailbox size limits in Exchange Online before migration to see which licenses you’ll need and which mailboxes might cause some problems.
• Communicate the change to end users. There are many differences between Exchange Server and Microsoft 365, even from the end user’s perspective.

How to migrate from Exchange 2016 and 2019 to Exchange Online using native tools

When moving away from Exchange 2016 or 2019 to the cloud, Microsoft lists the following migration scenarios:

• Cutover – which moves everything in one go.
• Full hybrid (a.k.a. remote move migration) – which “merges” your on‑premises and cloud environments and moves mailbox data in the background, trying to keep everything in sync all the time. This is the most complex deployment.
• Minimal hybrid (express migration) – this scenario creates a quick hybrid deployment.

Whichever migration method you choose (more on that below), the process essentially boils down to creating a migration batch, which is a sort of container holding necessary information on the migration’s scope, method, and schedule. Depending on your migration method, the batch may contain different information.

Note that the staged migration option, which you might know from the migration scenarios of old, is no longer available. However, if you want to move in stages, creating multiple migration batches in a hybrid deployment should be able to cover it.

Which migration method to choose

Cutover migration

Cutover is the most straightforward migration option, known since the first Exchange 2007 needed migration to Exchange Online. You could compare it to a simple cut-and-paste, thanks to which data is moved from on‑premises Exchange to Exchange Online.

There are two ways to create a migration batch in the cutover scenario:

1. In the Exchange admin center (Exchange Online EAC). On the Migration tab, you can create the batch, select the mailboxes to migrate, define the migration endpoint, and configure other migration options. For detailed step-by-step instructions, see this Microsoft article.
2. Using Exchange Online PowerShell. The New-MigrationBatch cmdlet supports a number of parameters corresponding to and extending beyond the options available in the Exchange Online EAC. See this Microsoft article for more details.

Hybrid migration

A hybrid migration requires a hybrid deployment between the on‑premises server and Exchange Online as a sort of intermediary step between the two environments – it lets you keep data both on‑premises and in the cloud, and synchronize it. Using the hybrid migration method should allow users to work with minimal disruption throughout the migration process.

To merge Exchange Server 2016/2019 with Exchange Online within a hybrid environment, you can use the Hybrid Configuration Wizard (HCW), available from the Exchange admin center (EAC). While the wizard is fairly straightforward, the configuration tasks it completes behind the scenes are not. Make sure you understand the purpose of each step, and analyze the HCW logs when you’re done to get an idea of how your environment has changed.

Once your environment is ready, you can start migrating mailboxes by creating a migration batch. Again, there are two ways to do this:

1. In the on‑premises Exchange admin center. Go to the Migration tab to add the batch, select the migration endpoint, choose user mailboxes to be migrated, and set up other migration options. You can also create the batch in the Exchange Online EAC, but the on‑prem workflow is more popular, and you’ll find instructions for it in this Microsoft article.
2. Using Exchange Online PowerShell. The New-MigrationBatch cmdlet supports a number of parameters corresponding to and extending beyond the options available in both the on‑premises and Exchange Online versions of the EAC. See this Microsoft article for more details.

Note that your hybrid deployment can be more or less permanent, but you shouldn’t use Exchange 2016 or 2019 if you want to keep it. The only recommended on‑premises Exchange server version is Exchange Server SE. So, if you need to stay hybrid, the recommended migration path would be migrating to Exchange Server SE first and then creating a hybrid environment.

Express migration (minimal hybrid)

The express migration is the quickest of the native migration scenarios. This method uses the Hybrid Configuration Wizard, like in full hybrid setup. However, minimal hybrid is meant to work similarly to the cutover migration, after which you decommission local Active Directory and Exchange Server.

In the express scenario, you run the migration from the Microsoft 365 admin center. For step-by-step instructions, see this Microsoft article.

How to migrate from Exchange 2016 and 2019 to Microsoft 365 with CodeTwo

“OK, but is there any easier way to migrate?” you may ask – and that’s a perfectly valid question. No native migration method is without its drawbacks. Each method requires manual labor and data collection. Limited reporting increases risk of data loss. Setting up a hybrid deployment can be tricky enough to give you a headache, and that’s before the actual migration even begins. If you’d rather avoid the extra complexity, a dedicated third-party solution like CodeTwo Office 365 Migration can simplify the process, overcome some of the limitations of Microsoft’s native tools and offer higher reliability.

With CodeTwo, you can migrate your on‑premises mailboxes to Exchange Online in a snap: no advanced setups and no PowerShell scripts are needed. The tool comes with a lightweight UI and guides you through the entire move step by step. The migration process is carried out automatically, with manual admin work kept to a minimum and no disruption to end users.

Watch the video below to see CodeTwo Office 365 Migration in action.

CodeTwo Office 365 Migration is widely recognized as the top migration tool on the market. Considered a powerful alternative to Microsoft’s native migration options, CodeTwo allows you to:

• Move your on‑premises mailboxes directly to Microsoft 365, regardless of your Exchange Server version and the size of your environment.
• Migrate all the contents and folder structure of your mailboxes, including emails, contacts, calendars, tasks, and more.
• Recreate public folders (ahead of EWS retirement in Exchange Online) or convert them to Microsoft 365 shared mailboxes.
• Automatically create and license target Microsoft 365 users.
• Easily match source and target mailboxes based on users’ AD attributes.
• Specify folder and time filters to get more granular control over the data to be migrated.
• Use a built-in scheduler to plan the migration in advance.
• Stay secure – the data that the program operates on is not accessible outside your organization. There are no additional third parties involved during the migration process.
• Get 24/7 support from CodeTwo’s award-winning Customer Success Team.

Click here to try CodeTwo Office 365 Migration for free.

Want to learn more about mailbox migrations to Microsoft 365? Get a free Conversational Microsoft 365 Migrations ebook by J. Peter Bruzzese.