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How to Resolve ‘Outlook Cleanup Not Working’ Issue Easily?

Ritu Roy | fix How to's Outlook outlook error remove duplicate files Technology | 7 minutes read | Modified on: 11-07-2025
Outlook cleanup not working

Are you struggling with the Outlook Cleanup tool not working properly? Whether your goal is to delete duplicate emails, archive old messages, or simply free up mailbox space, issues with Outlook’s cleanup features can seriously disrupt your workflow and lead to a cluttered inbox.

Features like Conversation Cleanup, Auto Archive, and manual cleanup options are designed to help keep your inbox organized and improve Outlook’s performance. However, when these cleanup tools fail, you might see duplicate emails piling up, old messages not being archived as expected, or deleted emails reappearing.

There is more to this issue than a small annoyance. A large and cluttered mailbox can slow down Outlook, make searching for emails more difficult, and even cause syncing or storage errors, especially if you handle a high volume of emails daily.

In this guide, we’ll walk you through all the effective solutions to fix Outlook cleanup problems, including why conversation cleanup may not be working and how to address missing auto-archive functions in Outlook 365. Plus, you’ll get handy tips to keep your mailbox clean and efficient going forward.

Why Is Outlook Cleanup Not Working?

Outlook relies on OST and PST files to store all your emails, contacts, calendars, and other data. When these files become corrupted, the cleanup tool may fail to remove duplicate emails or clean your mailbox effectively.

Large OST files, especially when managing thousands of emails or hefty attachments, can severely impact Outlook’s performance. In such cases, the cleanup process may freeze, skip items, or fail altogether. This is particularly common with shared or archived mailbox folders, where Outlook’s cleanup tool struggles with the sheer volume of data.

The Auto Archive feature is designed to automatically move or delete older emails. However, if Outlook isn’t closed properly or if Auto Archive isn’t configured correctly, cleanup may take longer than expected or may not work as intended.

Outlook regularly receives updates from Microsoft that include performance improvements and bug fixes. Running an outdated version of Outlook can often cause the cleanup functions to malfunction.

Third-party software, such as antivirus programs, custom email rules, or COM add-ins, may interfere with Outlook’s cleanup process. Some add-ins might block the cleanup entirely, while others slow down folder processing.

Lastly, while the Conversation Cleanup tool is useful, it has its limitations. It only removes redundant messages within email threads and does not delete standalone emails. Moreover, unread, flagged, or synchronized messages are typically excluded unless you specifically configure the tool to handle them.

How to Fix Outlook Cleanup Not Working Using an Automated Method

If Outlook’s built-in cleanup features fail to remove old or duplicate emails, an automated solution can save you time and effort. We recommend using CubexSoft Outlook Duplicate Remover, a reliable tool designed to quickly identify and delete all duplicate emails from your mailbox.

This software automatically detects Outlook files without requiring you to locate OST files or PST files manually. It also supports batch processing, allowing you to remove duplicate emails from multiple Outlook files at once without any limitations.

In addition to duplicates, CubexSpft PST Duplicate Remover helps you filter and clean out old items, ensuring your mailbox stays organized and clutter-free with minimal effort.

Steps to Fix Outlook Mailbox Cleanup Not Working

Download the software and follow the on-screen instructions to install it on your system.

Launch the program and click the Next button to select your configured Outlook mailbox data.

Choose the specific Outlook mailbox folder from which you want to remove duplicate emails.

Browse and review the PST file size at the destination path to ensure enough space is available.

Select the destination path where the cleaned mailbox data will be saved, then apply any desired Advanced filters to customize the cleanup process.

Finally, click Remove to begin fixing the Outlook cleanup issue and removing duplicate or old emails from your mailbox.

Helpful Features of the Recommended Software

  • Efficiently removes duplicate items from both corrupted OST and PST files.
  • Offers a user-friendly interface that is easy to navigate for both professionals and non-technical users alike.
  • Allows you to split the resulting PST file into manageable sizes such as 2GB, 4GB, 8GB, and more.
  • Enables searching for duplicate emails within a single folder or across multiple folders for thorough cleanup.
  • Provides powerful filter options, including selective export settings based on sender, recipient, CC, subject, body, attachments, date and time ranges, folder naming, excluding empty folders, and many other customizable parameters.

Now that you’ve removed duplicate emails using this tool, it’s time to address the Outlook cleanup not working issue by following the troubleshooting methods outlined in the next section.

Basic Fixes for “Outlook Cleanup Not Working”

If the Outlook cleanup feature isn’t functioning properly, don’t worry; many common issues can be resolved with a few simple steps. Try these quick fixes before moving on to more advanced troubleshooting:

#1: Enable and Configure Auto Archive Properly

  1. Select File > Options > Advanced after launching Outlook.
  2. Click on AutoArchive Settings and make sure AutoArchive is enabled.
  3. Check how often AutoArchive runs and what actions it performs (move or delete old items).
  4. Adjust the timeframe to archive or delete emails that are older than your preferred number of days.

#2: Empty Deleted Items and Junk Folders

  1. Right-click on the Deleted Items folder and select Empty Folder.
  2. To automate this, go to File > Options > Advanced.
  3. Under Outlook start and exit, check Empty Deleted Items folders when exiting Outlook.

#: Use Hard Delete for Stubborn Messages

  1. Select the emails that won’t delete normally.
  2. Press Shift + Delete to permanently remove these emails without sending them to the Deleted Items folder.
    Note: Use this with caution, as this action cannot be undone.

#4: Disable Problematic Rules or Add-ins

  1. Go to File > Manage Rules & Alerts and review your rules. Disable or delete any that might interfere with cleanup.
  2. Navigate to File > Options > Add-ins.
  3. At the bottom, select COM Add-ins and click Go. Disable any unnecessary or outdated add-ins that could be causing issues.

Repair Tools & Data File Fixes

#1: Using ScanPST (Inbox Repair Tool)

  1. Close Outlook completely.
  2. Navigate to the ScanPST executable located at:
    C:\Program Files\Microsoft Office\root\Office16\SCANPST.EXE
  3. Launch ScanPST and select the OST or PST file you want to repair.
  4. Click the Repair button to fix any minor corruption detected.

#2: Use Registry Tweak

  1. Press Win + R, type regedit, and press Enter.
  2. Navigate to the following registry key:
    HKEY_CURRENT_USER\Software\Microsoft\Office\<version>\Outlook\Preferences
  3. Create or modify a DWORD value named ArchiveIgnoreLastModifiedTime and set its value to 1.
  4. Click OK to save the changes.

Advanced Solutions When Cleanup Still Fails

#1: Reinstall or Repair Outlook/Office

  1. Open Control Panel and go to Programs > Programs and Features.
  2. Select Microsoft Office from the list.
  3. Click Change and choose the Repair option to fix any corrupted Outlook or Office files.

#2: Recreate Outlook Profile or Export/Import Mailbox

  1. Open Control Panel and navigate to Mail (Microsoft Outlook).
  2. Click Show Profiles, then click Add to create a new Outlook profile.
  3. Set the new profile as the default and relaunch Outlook.

#3: Open Outlook in Safe Mode

  1. Press Win + R, type Outlook.exe /safe, and press Enter.
  2. Check if emails appear correctly in Safe Mode.
  3. Go to File > Options > Add-ins.
  4. At the bottom, select COM Add-ins and click Go.
  5. Disable any suspicious add-ins and restart Outlook normally.

Preventive Measures to Avoid “Outlook Cleanup Not Working”

  • Keep Outlook Updated: Microsoft regularly releases updates to fix bugs, improve performance, and enhance compatibility with cleanup tools. To update Outlook, go to File > Office Account > Update Options > Update Now.
  • Run ScanPST Regularly: Use the Inbox Repair Tool (SCANPST.EXE) to detect and fix minor PST file corruptions that can affect Outlook’s performance and cause cleanup issues.
  • Manage Rules and Add-ins: Overly complex rules or outdated add-ins can disrupt email handling and cleanup processes. Periodically review and remove unnecessary or faulty add-ins and keep your rules simple and effective.
  • Empty Deleted Items and Junk Folders: Regularly clear out your Deleted Items and Junk Email folders to prevent mailbox bloat and improve cleanup efficiency.
  • Backup Your Outlook Data: Regular backups help protect your Outlook data and reduce the risk of corruption, ensuring you can restore your mailbox if any issues arise.

User Asked Queries

Q: Why is my Outlook Clutter Not Working?
Outlook Clutter has been replaced by Focused Inbox. If you don’t see Focused Inbox, ensure it is enabled in your settings. Clutter is no longer supported in newer Outlook versions or Microsoft 365 accounts.

Q: Why is the Outlook Junk Filter Not Working?
The Junk Filter may fail due to misconfigured rules or interference from add-ins. Check your Junk email settings, disable any conflicting rules, and ensure Outlook is updated. Also, verify that third-party spam filters are not overriding Outlook’s filter.

Q: How do I Enable Clean Up in Outlook?
Go to the Home tab, click on Clean Up, and select from Conversation, Folder, or Subfolder options. For more customization, navigate to File > Options > Mail > Conversation Cleanup. Ensure that Cleanup is not disabled by group policy or your administrator.

Q: Why is my Outlook Mailbox Still Full After Deleting?
If your Outlook mailbox is still full even after deleting emails, it’s likely because the deleted messages are still sitting in the Deleted Items folder, which continues to use storage space until it is emptied. To free up space, make sure to regularly clear this folder. Additionally, large email attachments and old messages may also be taking up significant space, so consider archiving or deleting them. If you’re using a Microsoft Exchange account, be aware that your mailbox quota may still include deleted items until they are permanently purged from the server.

Closing Remarks

This guide has covered multiple solutions to fix Outlook Cleanup not working issues. You can try all the approaches shared here for effective troubleshooting. However, if the problem stems from a corrupted OST file, manual fixes may not suffice. In such cases, using a reliable OST to PST Converter tool is recommended. It supports advanced recovery modes and generates healthy PST files, ensuring smooth access across all Outlook versions without the need for a specific Outlook profile.