Fix: “Your Mailbox Is Almost Full” in Microsoft 365 Outlook

A customer at a law firm contacted us after receiving the “Your mailbox is almost full” warning in Outlook. Their mailbox had reached 49 GB out of a 50 GB limit, and they were unsure what to do. Their internal IT had outlined several options but the customer wanted a cleaner solution that did not involve manually exporting emails to local storage. We enabled their Microsoft 365 Online Archive and applied a retention policy, which resolved the immediate issue and provided a long-term fix. Here is what caused it.

Symptoms

Users receive a high-importance email from Microsoft Exchange with the following warning:

Your mailbox is almost full.

49.06 GB / 49.5 GB

To make room in your mailbox, delete any items you don’t need and empty your Deleted Items folder. Learn more about storage limits.

In the Exchange Admin Center, the mailbox usage shows the mailbox approaching its quota:

Exchange Admin Center showing a mailbox at 98.21% capacity (48.62 GB of 49.5 GB).

You can also check mailbox storage in the Microsoft 365 Admin Center under the user’s Mail tab:

Microsoft 365 Admin Center showing mailbox storage at 86.43% (43.22 GB of 50 GB) on the user’s Mail tab.

As the mailbox approaches the limit, users may also experience:

• Unable to send emails (“Your mailbox is full” error at the send/receive quota)
• Outlook running slowly, especially when searching or loading folders
• Delays receiving new emails
• Outlook repeatedly prompting to reduce mailbox size

Affected Software

• Service: Microsoft 365 (Exchange Online)
• Platform: All Outlook clients (Windows, macOS, web, mobile)
• Default Limits: 50 GB for most Microsoft 365 Business plans, 100 GB for E3/E5

Cause

Microsoft 365 mailboxes have a storage quota (typically 50 GB for Business plans). Over time, mailboxes accumulate emails, attachments, calendar items, and contacts. The folders that consume the most space are usually Inbox, Sent Items, and Deleted Items (which many users never empty).

The warning is triggered when the mailbox reaches approximately 98% of its quota. At 100%, users can no longer send emails.

Resolution

What you can do yourself (no admin required)

These steps can be performed by any user directly in Outlook without needing to contact IT.

1. Empty Deleted Items: In Outlook, right-click the Deleted Items folder and select Empty Folder. This is often the single biggest space saver.
2. Empty Junk Email: Right-click the Junk Email folder and select Empty Folder.
3. Delete large attachments: In Outlook on the web, click your profile icon > View account > Storage to see your largest items. Sort by size and delete emails with large attachments you no longer need.
4. Clean up Sent Items: Sent Items often contains years of emails with attachments. Delete old sent emails you no longer need.

Long-term fix: Enable Online Archive (admin required)

Enabling the Online Archive requires an administrator. End users cannot enable this feature themselves. If you are not an admin, contact your IT team or managed service provider and ask them to enable the Online Archive on your mailbox.

The Microsoft 365 Online Archive creates a companion archive mailbox that appears directly in Outlook alongside your primary mailbox. This is the best solution for users who cannot delete old emails for compliance, legal, or business reasons.

The In-Place Archive appears as a separate mailbox in Outlook’s folder list.

Enable Online Archive via PowerShell:

# Check if archive is already enabled
Get-Mailbox -Identity "user@domain.com" | Select DisplayName, ArchiveStatus

# Enable the archive
Enable-Mailbox -Identity "user@domain.com" -Archive

# Verify it was enabled
Get-Mailbox -Identity "user@domain.com" | Select ArchiveStatus, ArchiveName

You can also enable it via the Exchange Admin Center under Recipients > Mailboxes > select the user > Others > Mailbox archive > Enable.

Archive mailbox sizes by plan:

• Microsoft 365 Business Basic/Standard: 50 GB archive (with Exchange Online Archiving add-on)
• Microsoft 365 Business Premium: Auto-expanding archive (starts at 100 GB, grows to 1.5 TB), included in the plan
• Microsoft 365 E3/E5: Auto-expanding archive (starts at 100 GB, grows to 1.5 TB), included in the plan
• Exchange Online Archiving add-on: Adds archiving to plans that do not include it (Business Basic, Business Standard, E1, F3)

Tip for admins: You can configure archives to be enabled automatically for any mailbox that reaches 90% capacity across your entire tenant:

# Auto-enable archive mailboxes org-wide when primary hits 90%
Set-OrganizationConfig -AutoEnableArchiveMailbox 

Create retention tags and apply a retention policy via PowerShell (admin)

Once the archive is enabled, create a retention policy that automatically moves old emails into the archive. This keeps the primary mailbox clean without any manual effort.

Step 1: Create a retention tag

# Create a Default Policy Tag that moves items older than 2 years to archive
New-RetentionPolicyTag -Name "GCIT-Archive-24m" -Type All `
  -RetentionEnabled $true -AgeLimitForRetention 730 `
  -RetentionAction MoveToArchive

Step 2: Create a retention policy and add the tag

# Create a retention policy
New-RetentionPolicy -Name "GCIT-Archive-Policy-24m" `
  -RetentionPolicyTagLinks "GCIT-Archive-24m"

Step 3: Apply the policy to a mailbox

# Apply the retention policy to a specific user
Set-Mailbox -Identity "user@domain.com" `
  -RetentionPolicy "GCIT-Archive-Policy-24m"

Step 4: Force the Managed Folder Assistant to process immediately

By default, the Managed Folder Assistant runs every 7 days. To process the mailbox immediately after applying a retention policy:

# Force immediate processing
Start-ManagedFolderAssistant -Identity "user@domain.com"

Newly enabled archives: If the archive was just enabled and Start-ManagedFolderAssistant returns an error, you may need to use the mailbox GUID instead of the email address. This is because the archive mailbox location has not fully propagated yet.

# Get the mailbox GUID and archive location
Get-Mailbox -Identity "user@domain.com" | Format-List *GUID, MailboxLocations

# Use the ExchangeGuid value to run the Managed Folder Assistant
Start-ManagedFolderAssistant -Identity "a]b1c2d3-e4f5-6789-abcd-ef0123456789"

The MailboxLocations property will show both the primary mailbox and archive mailbox locations with their GUIDs. Use the ExchangeGuid value if the UPN-based identity is not working.

Running Start-ManagedFolderAssistant in PowerShell to force the retention policy to process immediately.

Checking progress with PowerShell

You can monitor mailbox size before and after applying the retention policy using Get-MailboxStatistics:

# Check primary mailbox size
Get-MailboxStatistics -Identity "user@domain.com" | ft TotalItemSize

# Check archive mailbox size
Get-MailboxStatistics -Identity "user@domain.com" -Archive | ft TotalItemSize

Get-MailboxStatistics showing a mailbox at 49.17 GB (52,799,800,971 bytes), approaching the 50 GB quota.

Run this periodically after applying the retention policy to confirm the primary mailbox size is decreasing while the archive mailbox size is growing. After the Managed Folder Assistant processes the mailbox, you should see the mailbox usage start to decrease in the Exchange Admin Center as emails are moved to the archive.

Mailbox usage dropping from 98.21% to 98.14% shortly after the retention policy was applied and the Managed Folder Assistant ran.

Once an admin has enabled archiving and assigned a retention policy, users can manually apply archive and retention policies to individual emails or folders by right-clicking an item in Outlook and selecting Assign Policy. This is the one self-service option available to end users for managing their archive.

Users can right-click emails in Outlook and select Assign Policy to manually apply archive or retention policies.

Why Emails Are Not Moving to Archive (Litigation Hold)

If you have enabled the Online Archive and applied a retention policy but emails are not being moved to the archive, the most common cause is litigation hold or a legacy In-Place Hold.

When a mailbox is placed on litigation hold, Exchange preserves all mailbox content. While MoveToArchive retention actions should still work on mailboxes under standard litigation hold, legacy In-Place Holds can block archive moves entirely.

Check if holds are enabled:

# Check litigation hold
Get-Mailbox -Identity "user@domain.com" | Select DisplayName, LitigationHoldEnabled

# Check for legacy In-Place Holds
Get-Mailbox -Identity "user@domain.com" | Select InPlaceHolds

If emails are not moving to archive despite the policy being applied:

1. Verify the retention policy is assigned: Get-Mailbox -Identity user@domain.com | Select RetentionPolicy
2. Check that the archive is active: Get-Mailbox -Identity user@domain.com | Select ArchiveStatus
3. Force the Managed Folder Assistant: Start-ManagedFolderAssistant -Identity user@domain.com
4. If the mailbox has legacy In-Place Holds, these can block MoveToArchive actions. You may need to remove the hold (after legal approval) or migrate to a Purview retention policy instead

If the legal matter has been resolved and the hold is no longer required:

Set-Mailbox -Identity "user@domain.com" -LitigationHoldEnabled $false

Important: Only remove litigation hold after confirming with your legal team that the hold is no longer required. Removing a hold prematurely can have serious legal consequences.

For GCIT Managed Customers

If you are a GCIT customer, you should rarely encounter this issue. As part of our managed service, we proactively manage mailbox capacity across all customer tenants to prevent interruptions.

How GCIT prevents mailbox-full issues

GCIT deploys an automated mailbox retention policy system that runs daily across all managed tenants. Here is how it works:

• Daily monitoring: Our automation checks mailbox usage statistics for every user mailbox across all managed tenants
• Proactive archiving: When a mailbox reaches 90% capacity, we automatically apply a retention policy that moves emails older than 2 years to the Online Archive
• Progressive escalation: If the mailbox remains above 90% after two weeks, the policy is tightened progressively (18 months, 12 months, 9 months, 6 months) until the mailbox is back under control
• Safety checks: Before applying any policy, our system verifies that the Exchange Online Archive is active and checks the litigation hold status on the mailbox. Mailboxes with holds that could interfere with archiving are flagged for manual review
• Full audit trail: Every policy change is logged with the tenant, mailbox, previous policy, new policy, and mailbox size at the time of change

This means your team can focus on their work without worrying about storage warnings or manually cleaning out old emails. The system handles it automatically while preserving all email data in the archive for compliance and search purposes.

If you do receive a “mailbox almost full” warning, contact us and we will investigate why the automated policy has not resolved it.

Important Notes

• Do not delete emails for compliance reasons without checking your organisation’s data retention requirements first. Many industries (legal, healthcare, financial services) have mandatory email retention periods.
• The Online Archive is not the same as the Archive folder in Outlook. The Archive folder is just a regular folder in your primary mailbox. The Online Archive is a separate mailbox with its own storage quota.
• Outlook cached mode does not download the archive mailbox by default, so enabling archiving will not increase the size of your local Outlook data file (.ost).
• After enabling archiving and applying a retention policy, it can take up to 7 days for the Managed Folder Assistant to process the mailbox unless you force it with Start-ManagedFolderAssistant.
• Deleted Items do not auto-empty. Many users assume Deleted Items are automatically purged, but by default they are retained indefinitely and count towards the mailbox quota. Encourage users to empty Deleted Items regularly.
• Litigation hold and In-Place Holds can prevent retention policies from working as expected. Always check the hold status when troubleshooting archive issues.

Related Resources

• Microsoft Support: Manage my mailbox size
• Microsoft Learn: Enable archive mailboxes
• Microsoft Learn: Retention tags and retention policies
• Microsoft Learn: Auto-expanding archiving
• Microsoft Learn: In-Place Hold and Litigation Hold