Outlook Cleanup Not Working – Solved

  

Mark Regan
Published: July 8th, 2025 • 8 Min Read

Outlook Cleanup Tool like conversation cleanup, Auto Archive, and manual cleanup options are designed to streamline your inbox and faster performance. But when Outlook mailbox cleanup is not working, you may notice duplicate emails appear, old items not archiving, or deleted emails come back.

This issue isn’t a minor as a large size mailbox can affect Outlook performance, making searches emails harder, and even cause syncing or storage issues especially for those managing large volumes of communication daily.

In this guide, we will share all possible methods to solve Outlook cleanup conversation not working and share tips to prevent issues such as cleanup of old items missing in Outlook 365.

Why Outlook Cleanup Not Working?

• Outlook depends on its OST/PST files to store all Outlook data such as emails, contacts, calendars and other data. If these files get corrupted then Outlook cleanup doesn’t help you to remove duplicate emails.
• Oversized OST files can affect Outlook performance specially when you are managing thousands of emails or large size attachments, then cleanup get failed, freeze or skip items. Outlook Clean up tool can struggle with large size Outlook mailbox folders, especially in shared or archived mailboxes.
• Outlook’s Auto Archive features help automatically move or delete older emails. If it’s not shutdown properly or not configured correctly then it will take more time than the retention period to clean up.
• Microsoft offers regular updates which include bug fixes, faster performance. If you are using an outdated version, then Outlook clean up not working is a common issue.
• Custom email rules, COM Add-ins, or third party software(such as antivirus or archiving tools) can stop Outlook clean up functionality. Some add-ins can prevent the cleanup process while others could slow down the processing of folders.
• The Conversation Clean Up Tool is helpful but limited. It only removes redundant messages with email threads, meaning it won’t delete standalone or unrelated emails. Additionally, it won’t touch unread, flagged, or digitally synced messages unless specifically configured.

Helpful Features of Recommended Software

• This software can easily remove duplicate emails from corrupted OST and PST files.
• It offers a user-friendly interface to easily use by any professional or even any non technical users.
• You can also split the resultant PST file such as 2GB, 4GB, 8GB, and many more.
• With this wizard, you can search duplicate emails within a folder or across the folder.
• This tool also supports Filter options such as selective exported setting such as from, to, cc, subject, body, attachments, time, date range, saving folder naming, exclude empty folder and many more.
  Now you’ve removed duplicate emails from Outlook, it’s time to fix Outlook cleanup not working issue by following the approaches outlined in the next section.

Basic Fixes for “Outlook Cleanup Not Working”

If your Outlook cleanup feature isn’t working, don’t panic- many issues can be resolved with few simple adjustments. Here are quick fixes to try first before going to deep troubleshoot:

Method 1. Enable and configure Auto Archive properly

1. Open Outlook and navigate to file then press on Advanced.
   
2. Tap on Auto Archive Settings and make sure it is enabled and check how many times it runs and what action performed.
   
3. Adjust the timeframe to archive or delete items that are older than a set number of days.
   

Method 2. Empty Deleted Items and Junk Folder

1. Right-click on the deleted items folder and click on the Empty folder.
   
2. Consider setting Outlook to empty these folders automatically when you exit the app and press on file.
3. Then, Tap on Options and select Advanced and choose Outlook start and exit and hit on the Empty deleted items folder.
   

Method 3. Use Hard Delete for Stubborn Messages

1. Select emails and tap on Shift + Delete to permanently remove it.
   
2. Use it carefully, as it is a non-reversable process.

Method 4. Disable Problematic Rules or Add-ins

1. Navigate to file and click on Manage Rules and Alerts and review any articles rules.
2. Tap on file and click on options then hit on Add-ins and disable unnecessary or outdated add-ins using COM: Add-ins Manager.

Repair Tools & Data File Fixes

Approach 1. Using Run ScanPST(Inbox Repair Tool)

1. Close Outlook and navigate to SCANPST.EXE: C:\Program Files\Microsoft Office\root\Office16\SCANPST.EXE
2. Launch SCANPST Tool and select the OST/PST file as you want to remove.
3. Tap on the Repair button to fix minor corruption if found.

Approach 2. Use Registry Tweak

1. Press Win+R and type regedit and Hit Enter button.
2. Now, Navigate to : HKEY_CURRENT_USER\Software\Microsoft\Office\\Outlook\Preferences.
3. Create or Modify DWORD Value Name: ArchiveIgnoreLastModifiedTime, Value 1.
4. Press OK to apply changes.

Advanced Solutions When Cleanup Still Fails

Solution 1. Reinstall or Repair Outlook/Office

1. Navigate to the Control Panel and tap on Programs.
2. Hit on Program and Features and select Microsoft Office.
3. Tap on Change and choose Repair to make healthy Outlook files.

Solution 2. Recreate Outlook Profile or Export/Import Mailbox

1. Open Control Panel and Navigate to Mail(Microsoft Outlook).
   
2. Tap on Show Profiles and hit on Add to create a New Outlook profile.
   
3. Set it as default and relaunch Outlook.
   

Solution 3. Open Outlook in Safe Mode

1. Press Win+R and type Outlook.exe/safe.
   
2. Enter and check if in safe mode emails appear correctly.
3. Navigate to Options and click on Add-ins.
   
4. Hit on COM: Add-ins and tap on the Go button.
   
5. Now, Select suspicious Add-ins and remove them.
   

Preventive Measures to Avoid “Outlook Cleanup Not Working”

• Microsoft Outlook regularly patches to fix bugs, get faster performance, and enhance compatibility issues with cleanup tools by navigating to file and clicking on Office Account and hit on Update Options and press on Update Now.
• Run ScanPST.exe to fix PST minor corruption to fix Outlook performance and disrupt  communication.
• Overly complex rules or unnecessary Add-ins can interfere with email handling. Regularly remove outdated or faulty Add-ins or cleanup deleted items, or junk folder to keep maintained Outlook mailbox data.
• Backup Outlook data to keep your Outlook data protected and it also helps to prevent Outlook corruption.

Closing Remarks

This tutorial has illustrated various solutions to fix Outlook clean up not working. Users can try all approaches. If issues are not solved or found with your OST file corrupted then it can’t be done manually. So, you need to opt OST to PST Converter as it supports Recovery Mode and also offers a healthy PST file to easily access on all versions of Outlook without requiring any specific Outlook profile.