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Migrate Exchange 2013 to 2016 & Boost Your Server Experience

Published By Siddharth Sharma
Anuraag Singh
Approved By Anuraag Singh
Published On December 5th, 2023

In the modern business environment, it is vital to update your digital infrastructure. Especially the technology that millions rely on for email communication. One such situation is when businesses look to migrate Exchange 2013 to 2016. However, this process can be tough as we are talking about a decade-old server no longer supported by Microsoft. 

Nevertheless, you can make the challenging task easy by going through this article. It contains the complete procedure of data transfer between servers. First, let us look at what’s all new in the exchange version 2016 that makes an upgrade from the 2013 version worth it.

Why Migrate Exchange Server 2013 to 2016

First, the most obvious reason is that Microsoft has announced end of support for Exchange Server 2013.  Couple that with the fact that 2016 version is going to receive continued support from Microsoft for a few more years. You should start planning to shift your data from the previous version.

Other than that some more user-specific reasons are mentioned below.

  • If you work in an industry where there are strict regulatory and compliance demands, an improved Exchange version might be mandatory.
  • The ever-growing cyber attacks make a strong case for moving critical company data into a more secure environment like that of Exchange Server 2016.
  • Many Exchange 2013 to 2016 migration requests result from the need for a better collaboration mechanism i.e. direct integration with OWA introduced with the 2016 version.
  • Moreover, the already existing features like DLP receive an upgrade(80 new notification parameters) which makes them more powerful and easy to use.

Also Read: Learn to Migrate Zoho Mail to Office 365 & Level up the Email Experience

Now it’s time to focus on the prerequisites, No matter which method you end up using the preparation for both is the same.

Prerequisites to Migrate Mailbox Exchange 2013 to 2016

Any IT Admin who is responsible for handling the server upgrade must first check and validate the following:

  • The current system configuration fulfills the minimum requirements for setting up an Exchange 2016 server. Such as 64-bit, CPU, 8GB RAM, Windows Server 2008 or higher, etc.
  • Set up a new AD Forest and build a target environment for Exchange 2016. Ensure that Send Connector, Domains, and internal & external URLs are all configured appropriately.
  • Take a backup of all the data currently residing on the host server. It is to provide an additional layer of safety in case of data corruption issues during migration.
  • Install and set up the Exchange Version 2016 on your local machine with the exact same data size constraints as the 2013 version.

Manual Methods of Transfering Exchange Data From 2013 to 2016 Version 

There are two separate methods for manual data migration we cover them one by one.

Steps to Migrate Exchange Server 2013 to 2016 Using the EAC:

  • Login to the EAC portal using admin credentials
  • Open the pane on your lefthand side and click “Recipients”.
  • From the dropdown menu pick the “Migration” option.
  • Click the “+ (New)” button to create a new migration batch.
  • Within the “Select a migration type” window pick “Move to a different database”.
  • Next, click on the “Add” button and select the mailboxes.
  • Configure a migration endpoint. Choose the Exchange Server 2016 as the version and fill in other credentials as well.
  • Don’t make any changes to the default prompts (target, item, mailbox)  unless required, and click Next.
  • Upon review completion hit the “Finish” button and commence with the migration.
  • To look at the current status of the migration, return to the “Recipient” page under “Migration“ to view the status of the current batch.

Using PowerShell Commands:

Step 1. Launch and link the PowerShell module with EAC using the below-mentioned code snippet as a template:

Import-Module ExchangeOnlineManagement

Connect-ExchangeOnline -UserPrincipalName <UPN> [-ExchangeEnvironmentName <LocalExchangeServer>] [-ShowBanner:$false] [-DelegatedOrganization <OrganizationName>] [-SkipLoadingFormatData]

Step 2. Create a new migration endpoint using: 

New-MigrationEndpoint -Name Exchange2013 -ExchangeRemote -Autodiscover -EmailAddress admin@domain.com -Credentials (Get-Credential domain\admin)

Step 3. Allow the system  to read the CSV file  


Step 4. Build a new batch for migration and start with the data transfer:

New-MigrationBatch -CSVData $csvData -Timezone "Pacific Standard Time" -Name ExchangeMigration -SourceEndpoint Exchange2016 -TargetDeliveryDomain "mail.newdomain.com"

Step 5. Check for migration status:

Get-MigrationUserStatistics -Identity ExchangeMigration -Status | Format-List

Automated Method of Exchange 2013 to 2016 Migration

To outright skip the tedious and error-prone manual approaches we have a professional tool at your disposal. The expert recommended SysTools Exchange to Exchange Migration Tool as one of its one-of-a-kind data transferring utility. It combines the simplicity of a user-friendly interface with cutting-edge migration algorithms to provide a complete package. 

Download Now Purchase Now

  • No technical expertise or deep knowledge is required to use the tool for migration.
  • Intelligent filters to mark Type, select Date, and assign priority to the data.
  • Get a birds-eye view of the migration in 3 sections( Pending, In Progress, Complete).
  • Gain the ability to move data in different scenarios using (retry, re-run, and delta).
  • Add users via Fetching, Importing a CSV, or Downloading a template.
  • Set up real-time updates that appear directly on your mail with SMTP protocol.

No other alternative on the market offers so many features at such a competitive price point. Let’s look at the steps for using the tool.

Automated Steps to Migrate Exchange 2013 to 2016 Easily

Step 1. Download the tool from the link, Open it, and Select Exchange as both source and target.

Select Source and Destination as Exchange

Step 2. Scroll towards the Workload Area and Mark the Check Boxes next to the data type you wish to transfer, Also specify the Date using the Filter if need be.

Select Workload and Apply Date Filters

Step 3. Go to the Source tab specify the server version as 2013, fill in other relevant details Validate, and press Next.

Validate Source

Step 4. Same as the last step, visit the target page, mention 2016 as the server version enter other information, Validate, and proceed by hitting Next.

Select Exchange Server Version as 2016

Step 5. Attach users by either directly Fetching them from the server, otherwise, you can Import a premade CSV file, or edit the template present in the Download button.

Add Users

Step 6. Finally, preview the user list select the ones required according to priority, Validate, and hit the Start Migration button.

Start Migration

The tool automatically does the rest. After the migration ends you must perform some post-migration steps regardless of the method you choose.

Post Migration Tasks to Perform

Our work is not done yet but once we complete the below-mentioned steps we will be free to use the Exchange Server 2016.

Adjust the MX Records: These records decide which emails go in which mailbox so updating them to point toward the correct mailbox is necessary to regain normal server functionality.

Decommission Exchange 2013: This is the last step in the entire process. It makes sure that our previous server is no longer live and thus prevents any errors during email communication.

Read More: How to Migrate Exchange 2010 to 2016 & Upgrade the Exchange Server


Every user who followed this tutorial on how to migrate Exchange 2013 to 2016 now has a complete understanding of the process. Here we gave you the list of every detail to check for before, during, and after migration to make the task as smooth as possible. Moreover, an automated utility is included which reduces both the time and effort required for the migration.