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The standard, free version of Malwarebytes Anti-Malware just functions as an on-demand scanner. In other words, it doesn’t run automatically in the background. Instead, it only does something when you launch it and click the Scan button.
This version of Malwarebytes shouldn’t interfere with your antivirus program at all. Just install it and occasionally launch it to perform a scan and check for the “potentially unwanted programs” almost no one actually wants. It will find and remove them. Using an anti-malware program as an on-demand scanner is a safe way to get a second opinion.
You shouldn’t have to do any extra configuration here. If Malwarebytes reports some sort of error removing a piece of malware it finds, you could potentially pause or disable real-time scanning in your main antivirus program to prevent it from interfering, and then reenable real-time scanning right after. But even this shouldn’t be necessary, and we’ve never heard of anyone encountering a problem like this one.
Run Malwarebytes in Side-by-Side Mode
Starting with Malwarebytes 4, the Premium version of Malwarebytes now registers itself as the system’s security program by default. In other words, it will handle all your anti-malware scanning and Windows Defender (or whatever other antivirus you have installed) won’t run in the background.
You can still run both at once if you like. Here’s how: In Malwarebytes, open Settings, click the “Security” tab, and disable the “Always register Malwarebytes in the Windows Security Center” option.
With this option disabled, Malwarebytes won’t register itself as the system’s security application and both Malwarebytes and Windows Defender will run at the same time.