Exchange 2016 Migration – Complete Step-by-Step Guide for Office 365, Exchange 2019 & Hybrid Environments

Migrating from Exchange Server 2016 can be a daunting process—especially when you’re moving to Office 365, Exchange 2019, or even setting up a hybrid environment. Between managing mailboxes, maintaining uptime, and ensuring data integrity, there’s a lot to juggle.

In this guide, we’ll walk you through everything you need to know about Exchange 2016 migration—from planning and preparation to execution and post-migration checks. We’ll also show you how Shoviv Exchange Migration Tool can make the process significantly easier, faster, and more reliable.

Why Organizations Migrate from Exchange 2016

While Exchange 2016 is still a robust email server, there are several reasons businesses choose to migrate:

• End of mainstream support from Microsoft
• Desire for cloud-based flexibility via Office 365
• Moving to Exchange 2019 for better performance and modern features
• Compliance, security, and disaster recovery improvements
• Mergers, acquisitions, or organizational restructuring

Types of Exchange 2016 Migrations

1. Exchange 2016 to Office 365 (Microsoft 365) Migration

Migrating from on-premises Exchange 2016 to Office 365 offers:

• Scalability
• Reduced infrastructure costs
• Access from anywhere

Migration methods include:

• Cutover Migration – Move all mailboxes at once (best for small organizations)
• Staged Migration – Gradually move batches of mailboxes
• Hybrid Migration – Maintain both environments temporarily for seamless transition

2. Exchange 2016 to Exchange 2019 Migration

For organizations that prefer to stay on-premises, upgrading to Exchange 2019:

• Delivers better performance with modern hardware
• Offers enhanced security
• Supports larger mailboxes

3. Exchange 2016 to Exchange 2016 (Cross-Forest or Same-Forest)

You might need this migration during:

• Server hardware upgrades
• Data center moves
• Merging Exchange environments between organizations

4. Hybrid Exchange Migration

Hybrid setups allow you to:

• Keep some mailboxes on-premises
• Move others to Office 365
• Maintain unified management and global address lists

Challenges in Exchange 2016 Migration

Migrating Exchange isn’t always straightforward. Common hurdles include:

• Downtime risk during cutover
• Data integrity concerns
• Mailbox size limitations
• Permission mismatches
• Calendar sharing issues
• Complex public folder migration

Pre-Migration Checklist for Exchange 2016

Before starting, ensure:

1. Environment health check – Use Get-ExchangeServer and run Microsoft’s Exchange Best Practices Analyzer.
2. Backup all mailboxes and databases.
3. Check DNS, Autodiscover, and SSL certificates.
4. Verify free mailbox space and reduce oversized mailboxes if needed.
5. Update Exchange to the latest CU (Cumulative Update).

Step-by-Step Migration from Exchange 2016 to Office 365

1. Assess current infrastructure
• Inventory users, groups, and public folders.
• Review hybrid readiness.
2. Select migration type
• Cutover, staged, or hybrid.
3. Prepare Office 365 tenant
• Add your domain in Microsoft 365.
• Configure DNS records.
4. Set up directory synchronization (for staged/hybrid migrations).
5. Migrate mailboxes
• In Exchange Admin Center (EAC), create a migration batch.
• Monitor progress.
6. Switch DNS and finalize cutover
• Update MX records to point to Office 365.
7. Post-migration tasks
• Remove old mailboxes and databases.
• Decommission the Exchange 2016 server if not needed.

How Shoviv Exchange Migration Tool Simplifies the Process

Manually handling Exchange 2016 migration is time-consuming and risky. Shoviv Exchange Migration Tool offers:

• Direct migration from Exchange 2016 to Office 365, Exchange 2019, or another Exchange 2016 server.
• No downtime – Migrate in the background without affecting users.
• Incremental migration – Only migrate new or changed items.
• Public folder migration support.
• Advanced filters to migrate specific mailboxes, folders, or date ranges.
• User-friendly interface – No complex PowerShell scripts needed.

Best Practices for Exchange 2016 Migration

• Run migrations in off-peak hours to minimize disruption.
• Communicate migration plans to end-users.
• Test migration on a small batch first.
• Keep both environments available until you verify all data is intact.
• Document every step for future reference.

Final Thoughts

Migrating from Exchange 2016 can be challenging, but with careful planning, the right tools, and a phased approach, you can ensure a smooth transition—whether you’re moving to Office 365, upgrading to Exchange 2019, or setting up a hybrid environment.

If you want to skip the headaches of manual migration, Shoviv Exchange Migration Tool is built to handle large-scale, complex Exchange 2016 migrations with speed, security, and zero downtime.