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SOLVED: Office 365 mailbox not showing in Exchange hybrid server admin center

Friday, 14 October 2022

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How to fix an issue where an Office 365 user mailbox shows in Exchange online but not on the Exchange hybrid server (on-premises) using PowerShell Enable-RemoteMailbox

I recently had to troubleshoot an issue where a user mailbox still exists in Office 365 even though the Exchange online license had been removed from the user account. The orphaned mailbox shows in Exchange online but does not show in the on-premises Exchange hybrid server admin center. In this case, the mailbox also had litigation hold enabled

Problem: Office 365 mailbox not showing on Exchange hybrid server

The Office 365 user account has an Office 365 E3 license with only Microsoft 365 Apps selected - no Exchange online license.

The mailbox still exists in Office 365 Exchange online

Mailbox does not exist on Exchange hybrid server on-premises

Solution: Steps to fix Office 365 not showing in Exchange admin center

You should wait 5-10 mins between each step to allow time for the changes to update. Making changes enabling and disabling mailboxes too quickly can cause issues.

1. Temporarily re-enable the mailbox

On Exchange hybrid server
Open Exchange Management Shell

Temporarily re-enable the mailbox for the user account

Enable-RemoteMailbox user@domain.com -RemoteRoutingAddress user@domain.mail.onmicrosoft.com

2. Run AD connect sync

On AD connect server
Run AD Sync

Start-ADSyncSyncCycle -PolicyType Delta

3. Temporarily re-assign Exchange online license

In Office 365 admin portal
https://portal.office.com

Temporarily re-assign an Exchange online license to the user account in Office 365

4. Remove holds on the mailbox

# Connect to Exchange online PowerShell
Connect-EXOPSSession -UserPrincipalName admin@domain.com

# Remove holds on the mailbox
Set-Mailbox user@domain.com -SingleItemRecoveryEnabled $false
Set-Mailbox user@domain.com -RetentionHoldEnabled $false
Set-Mailbox user@domain.com -LitigationHoldEnabled $false

5. Remove Office 365 licenses

Remove all licenses from the user account in Office 365

6. Disable mailbox on Exchange hybrid

On Exchange hybrid server
Open Exchange Management Shell

Disable-Remotemailbox user@domain.com

7. Run AD sync again

On AD connect server
Run AD Sync

Start-ADSyncSyncCycle -PolicyType Delta

The mailbox has now been removed from both Office 365 Exchange online and Exchange on-premises.
Re-assign an Office 365 E3 license (M365 apps only) to the user account

This problem was most likely caused by the user being under litigation hold and removing the Office 365 Exchange online license before running Disable-Remotemailbox on the Exchange hybrid server.

Running Disable-RemoteMailbox removes Exchange attributes from the AD user and removes the mailbox in Office 365.

Making changes enabling and disabling mailboxes without waiting for AD sync can also cause issues.