Resolved: Hybrid Exchange Duplicate (Ghost) Mailbox Created After Assigning Exchange Online License

Summary

During a hybrid Exchange migration, a user’s mailbox failed to migrate and mail flow broke due to a duplicate (ghost) mailbox automatically created in Exchange Online.

Root Cause

An Exchange Online Plan 2 license was mistakenly assigned to the user before migration. Azure AD sync then provisioned a cloud mailbox, even though the user already had an on-prem mailbox. This caused a hybrid mismatch — the user appeared in both environments, and migration failed with mailbox lookup errors.

Resolution Steps

• Removed the Exchange Online Plan 2 license from the user account.
• Forced a DirSync (AAD Connect) synchronization.
• Verified that the mailbox existed only on-prem via PowerShell

Get-Mailbox -Identity email address removed for privacy reasons | fl Name,RecipientTypeDetails,ExchangeGuid

• Confirmed the ghost mailbox was removed from Exchange Online.
• Re-ran migration batch successfully to Exchange Online.

Verification

Get-MailboxStatistics -Identity email address removed for privacy reasons | fl TotalItemSize,ItemCount,LastLogonTime

Ensure only one mailbox object exists and mail flow routes correctly.

Prevention Tips

• Don’t assign Exchange Online licenses to hybrid mailboxes before migration.
• Always verify mailbox location prior to assigning any license.
• Use PowerShell or EAC to check where the mailbox resides (on-prem vs. cloud).

Environment

• Hybrid Exchange Deployment
• Exchange 2016 On-Premises
• Exchange Online (M365)
• Azure AD Connect

This issue is not caused by connectors or mail flow settings, but by improper licensing before migration. Removing the license and resyncing resolves the ghost mailbox problem.