Mastering Mailbox Cleanup and Holds in Exchange Online

As businesses increasingly rely on Microsoft 365 for email management, Exchange Online mailboxes remain a cornerstone of productivity. However, even in 2025, users and administrators encounter persistent challenges that can disrupt workflows. This article explores the most common problems affecting Exchange Online mailboxes, drawing on recent reports, official Microsoft guidance, and user experiences.

What are MRM Retention Policies

MRM (Messaging Records Management) Retention Policies in Exchange are a system used to automatically manage the lifecycle of email messages and other mailbox items. They help organizations control mailbox growth, comply with legal or regulatory requirements, and ensure important data is retained while unnecessary items are deleted.

How the MRM Process Works

Exchange Online uses the Managed Folder Assistant (MFA) to automatically apply mailbox retention policies and perform cleanup in the background.
MFA ensures deleted or expired items are purged according to the organization’s policy.
Normal email lifecycle:
- When a user deletes an item, it moves to the Deleted Items folder.
- When the item is deleted again or emptied, it moves to the Recoverable Items folder (“dumpster”).
- MFA then applies retention or purge logic to delete items that exceed the retention period.
If ElcProcessingDisabled is set to True (either at the mailbox or organization level), this automated cleanup process will not run. Deleted content remains in the Recoverable Items folder indefinitely until the setting is re-enabled or manual cleanup is performed.

Settings That Can Affect or Delay MRM Cleanup

ElcProcessingDisabled: Disables the automated MRM process for the mailbox or the entire organization.
RetentionHoldEnabled: Temporarily pauses retention policies (often used during investigations or when users are on leave).
LitigationHoldEnabled: Retains all content indefinitely for compliance or legal reasons; cleanup cannot proceed while enabled.
DelayHoldApplied/DelayReleaseHoldApplied: Temporary system holds applied during retention policy or compliance label changes; may delay MRM.
Purview Retention Policies: Retain or delete items based on compliance settings. If the mailbox is still in policy scope, cleanup is blocked.
SingleItemRecoveryEnabled: Allows recovery of deleted items within a defined window before permanent purge.
RetainDeletedItemsFor: Specifies how long deleted items are kept in the Recoverable Items folder before permanent purge.

Check and Clear Holds

Run the following command to check if any holds are applied:

Get-Mailbox "UPN" | FL Hold

Then review and adjust based on the results:

If Litigation Hold is enabled
Cleanup cannot occur until removed. To temporarily disable it (if approved by compliance):

Set-Mailbox -Identity "UPN" -LitigationHoldEnabled $false

If Retention Hold is enabled
Pauses cleanup; remove it using:

Set-Mailbox -Identity "UPN" -RetentionHoldEnabled $false

If Delay Hold flags exist
Clear them using:

Set-Mailbox -Identity "UPN" -RemoveDelayHoldApplied

Set-Mailbox -Identity "UPN" -RemoveDelayReleaseHoldApplied

If mailbox is still in scope of Purview Retention Policies
Temporarily exclude it from those policies:

Set-RetentionCompliancePolicy -Identity "Exchange Retention Policy" -AddExchangeLocationException "UPN"

Set-RetentionCompliancePolicy -Identity "Teams chats Policy" -AddTeamsChatLocationException "UPN"

After adjustments, trigger MRM again:

Start-ManagedFolderAssistant -Identity "UPN" -FullCrawl -AggMailboxCleanup

Steps to check the MRM Process

Run the following commands to restore automatic cleanup for the mailbox UPN:

Connect-ExchangeOnline

Connect-IPPSSession

Get-Mailbox -Identity "UPN" | FL ElcProcessingDisabled

Set-Mailbox -Identity "UPN" -ElcProcessingDisabled $false

Get-OrganizationConfig | FL ElcProcessingDisabled

# If result is True, run this command:

Set-OrganizationConfig -ElcProcessingDisabled $false

Adjust Retention to Speed Up Cleanup

The mailbox UPN currently has a 30-day retention period.

To speed up cleanup, you can temporarily set it to 0 days and restore it after cleanup completes:

Set-Mailbox -Identity "UPN" -RetainDeletedItemsFor 0 -SingleItemRecoveryEnabled $false

Start-ManagedFolderAssistant -Identity "UPN" -FullCrawl -AggMailboxCleanup

Restore Default Protections (After Cleanup Completes)

Once the mailbox size is reduced and items are cleared, restore standard settings:

Set-Mailbox -Identity "UPN" -RetainDeletedItemsFor 30 -SingleItemRecoveryEnabled $true

Enable Litigation Hold again if it was active before

Set-Mailbox -Identity "UPN" -LitigationHoldEnabled $true

Set-RetentionCompliancePolicy -Identity "Exchange Retention Policy" -RemoveExchangeLocationException "UPN"

Set-RetentionCompliancePolicy -Identity "Teams chats Policy" -RemoveTeamsChatLocationException "UPN"

Start-ManagedFolderAssistant -Identity "UPN"

Summary

The Managed Folder Assistant (MRM) performs retention and cleanup automatically.
When ElcProcessingDisabled or any hold is active, MRM cannot delete items.
Retention policies and litigation hold take precedence and will preserve items until removed.
Adjusting retention temporarily, clearing holds, and re-triggering MRM allows cleanup to resume normally.

Notes

Both settings can pause retention actions, but in different ways. ElcProcessingDisabled fully stops the system from processing any retention policies, while RetentionHoldEnabled keeps the process running but temporarily skips applying deletions or archiving. In short, the first one turns retention off completely, and the second one pauses it safely without disabling the feature.
You can run the Managed Folder Assistant (MFA) manually to speed up retention and cleanup processes in the mailbox. The -HoldCleanup switch focuses on clearing items affected by holds after they’ve been removed, while the -FullCrawl -AggMailboxCleanup switch performs a complete scan of the mailbox to apply new retention or archive policies faster. Running both helps ensure that all retention changes take effect promptly.
Don't run the -AggMailboxCleanup command too many times.
Sometimes, it can take up to 3-5 days because the size of the mailbox is huge, so run the command daily 1 time

Most common Mailbox Issues related to Storage

Cannot delete Items (After refresh, deleted items re-appear)
Cannot schedule meetings/receive meetings
3) Storage is full, but the primary or Archive mailbox has space

Cause: The Recoverable Items folder is full.

Check the Recoverable Items folder status

Get-MailboxFolderStatistics -Identity "UPN" -FolderScope RecoverableItems | FT Identity, ItemsInFolderAndSubfolders, FolderAndSubfolderSize -AutoSize

Check whether any HOLD is active on the Mailbox

Get-Mailbox "UPN" | FL Hold

If any HOLD is active, disable temporarily.

Delete the Recoverable Folder.

· Set-Mailbox -Identity "UPN" -RetainDeletedItemsFor 0 -SingleItemRecoveryEnabled $False

· Start-managedfolderassistant "UPN" -fullcrawl -aggmailboxcleanup

4) If the MRM retention policy is not working when we enable Archive for the mailbox

Check the mailbox has Retention Hold active.

Temporarily disable and manually move the mailbox data.

Check the mailbox statistics

Get-MailboxFolderStatistics -Identity "UPN" | Select Name, FolderPath, FolderSize, FolderAndSubfolderSize

Move Mailbox forcely

Start-ManagedFolderAssistant -identity "UPN"

Start-ManagedFolderAssistant -identity "UPN" -FullCrawl

Note: If still mails are not moving to Archive, disable SingleItemRecovery and try again.