Malwarebytes is primarily a scanner that scans for and removes malicious software, including rogue security software, adware, and spyware. Malwarebytes scans in batch mode, rather than scanning all files opened, reducing interference if another on-demand anti-malware software is also running on the computer.

Malwarebytes is available in both a free and a premium paid version. The free version can be run manually by the user when desired, whereas the paid version can perform scheduled scans, automatically scan files when opened, block IP addresses of malicious web sites, and scan only those services, programs and device drivers that are currently in use.

On December 8, 2016, Malwarebytes Inc. released version 3.0. This includes protection against malware, ransomware, exploit, and malicious websites.

In November 2019, version 4.0 was released, featuring a new user interface and the Katana scanning engine.