Introduction

Microsoft Exchange has always been the backbone of enterprise communication. With Exchange 2016, businesses gain advanced features such as better compliance, improved Outlook web experience, and enhanced data security. That’s why many organizations are now planning an Exchange 2013 to 2016 migration.

While Microsoft supports this upgrade path, the migration process is not without challenges. This blog provides a detailed, step-by-step guide, explores the common issues admins face, and highlights how using a professional tool for ensures a seamless transition.

Why Upgrade from Exchange 2013 to 2016?

Migrating from Exchange 2013 to 2016 offers:

• Better Outlook Web Access (OWA) with a modern UI

• Improved search performance for large mailboxes

• Simplified coexistence with hybrid setups

• Advanced data loss prevention (DLP) features

• Higher availability and reduced failover time

These improvements make Exchange 2016 a reliable step up from 2013.

Common Challenges in Exchange 2013 to 2016 Migration

Despite being a supported migration path, admins often face:

1. Downtime Risks – Any interruption may affect user productivity.

2. Large Mailbox Sizes – Can cause performance issues or migration failures.

3. Public Folder Migration – Maintaining hierarchy and permissions is complex.

4. Coexistence Complexity – Running 2013 and 2016 together during transition requires proper planning.

5. Limited Reporting – Native methods don’t provide detailed migration reports.

Manual Method for Exchange 2013 to 2016 Migration

The migration typically involves these steps:

1. Prepare the Environment

   • Install Exchange 2016 prerequisites (Windows roles, .NET Framework, UCMA).

   • Ensure Active Directory schema is updated.

2. Install Exchange 2016

   • Deploy Client Access and Mailbox roles.

   • Configure namespaces (Autodiscover, OWA, ECP).

3. Coexistence Setup

   • Configure load balancing between Exchange 2013 and 2016.

   • Test mail flow and connectivity.

4. Move Mailboxes

   • Use Exchange Admin Center (EAC) or PowerShell to migrate user mailboxes.

5. Migrate Public Folders

   • Export and re-map public folders to Exchange 2016.

6. Decommission Exchange 2013

   • After testing and verification, uninstall Exchange 2013.

Limitations of Manual Migration:

• Time-consuming for large organizations

• High risk of errors and downtime

• No incremental migration (failures require redoing the process)

Best Way to Simplify Migration

For businesses that want to avoid downtime and errors, the Shoviv Exchange Migration Tool provides a much safer path.

Key Benefits:

• Direct migration from Exchange 2013 to 2016 without complexity

• Incremental migration – resumes interrupted jobs without duplication

• Bulk mailbox support – migrate thousands of mailboxes at once

• Zero downtime – users keep working while migration runs

• Public folder support – with intact hierarchy and permissions

• Detailed reports for compliance and tracking

This makes Shoviv the best choice for organizations planning Exchange upgrades.

Best Practices for Exchange 2013 to 2016 Migration

• Perform a pre-migration audit of mailboxes and permissions.

• Test migration with pilot users before full deployment.

• Always keep backups ready.

• Communicate clearly with end-users about expected changes.

• Use a professional tool for a risk-free migration.

Conclusion

The Exchange 2013 to 2016 migration is a critical step for organizations looking to modernize their messaging environment. While Microsoft’s native methods are available, they are often complex, error-prone, and time-consuming.

Using a professional solution like the Shoviv Exchange Migration Tool ensures a seamless, secure, and downtime-free migration experience — making it the smartest choice for IT admins in 2025.