If your Malwarebytes scan is stuck at 99%, you’re not alone. Many users experience this issue during Threat Scan or Custom Scan, where the progress bar freezes near completion and doesn’t move forward. While it may look like the scan has completely stopped, the problem is often caused by system delays, file conflicts, or minor software glitches.
In this guide, you’ll learn why Malwarebytes scans get stuck at 99% and how to fix the issue step by step.
Why Malwarebytes Gets Stuck at 99%
There are several common reasons this happens:
Large or compressed files being scanned
Corrupted system files
Conflicts with other antivirus programs
Outdated Malwarebytes version
Insufficient system resources
Hard drive errors
Background programs interfering
When the scan reaches 99%, Malwarebytes is often analyzing the final files, which may take longer than expected.
Step 1: Wait a Little Longer
Before assuming the scan is frozen, give it some time.
Sometimes Malwarebytes appears stuck at 99% but is still processing:
Large archive files (ZIP, RAR, ISO)
System memory objects
Deep-rooted system directories
Wait at least 10–20 minutes to confirm whether it’s truly stuck.
Step 2: Restart Malwarebytes
If the scan remains frozen for an extended period:
Close Malwarebytes completely.
Open Task Manager and ensure no Malwarebytes processes are running.
Restart the program.
Run the scan again.
In many cases, restarting clears temporary glitches.
Step 3: Restart Your Computer
A simple system reboot can refresh background services and fix temporary conflicts.
Save your work.
Restart your PC.
Launch Malwarebytes.
Run the scan again.
This often resolves minor software conflicts.
Step 4: Update Malwarebytes
An outdated version of Malwarebytes can cause scanning issues.
To update:
Open Malwarebytes.
Go to Settings.
Click “Check for updates.”
Install any available updates.
Restart your computer.
After updating, try scanning again.
Step 5: Disable Other Antivirus Programs
If you have another antivirus installed, it may conflict with Malwarebytes during scanning.
Temporarily disable:
Real-time protection in other antivirus software
Third-party security tools
Then rerun the scan.
Running multiple security programs simultaneously can slow down or freeze scans.
Step 6: Run Malwarebytes as Administrator
Running the program with full system permissions can help prevent scan freezes.
Close Malwarebytes.
Right-click the Malwarebytes icon.
Select “Run as administrator.”
Start the scan again.
This gives Malwarebytes proper access to system files.
Step 7: Check Your Hard Drive for Errors
Hard drive issues can cause scans to freeze near completion.
To check your drive:
Open Command Prompt as administrator.
Type:
chkdsk /fPress Enter.
Restart your computer if prompted.
This process checks and repairs disk errors that may be causing the issue.
Step 8: Use the Malwarebytes Support Tool
If the problem persists, the installation files may be corrupted.
Malwarebytes provides a Support Tool that can:
Repair the program
Perform a clean uninstall
Reinstall the latest version
Download the Support Tool from the official website, run it, and choose the repair or clean install option.
After reinstalling, run a new scan to see if the issue is resolved.
Step 9: Exclude Problematic Files
Sometimes a specific file causes the scan to freeze repeatedly.
If the scan consistently stops at the same file:
Note the file name (if visible).
Add it to the exclusion list temporarily.
Run the scan again.
Be cautious when excluding files and only do so if you’re confident the file is safe.
Step 10: Check System Resources
Low RAM or CPU overload can slow down scanning dramatically.
Before running a scan:
Close unnecessary applications
Disable heavy background programs
Free up disk space
This allows Malwarebytes to run more smoothly.
Final Thoughts
When Malwarebytes gets stuck at 99%, it’s usually caused by large files, system conflicts, or minor software issues—not necessarily malware.
By waiting patiently, restarting the program, updating the software, checking disk errors, and disabling conflicting antivirus tools, you can usually resolve the issue quickly.
If the problem continues even after reinstalling, contacting Malwarebytes support is the best next step. With proper troubleshooting, your scans should complete successfully and keep your system fully protected.