It has offices in Santa Clara, California; Clearwater, Florida; Tallinn, Estonia; Bastia Umbra, Italy; and Cork, Ireland.

[6] CEO and founder Marcin Kleczynski, originally from Poland, was still a teenager attending high school in Bensenville, Illinois, and was working as a technician in a computer repair shop in Chicago.

[9] In 2006, Kleczynski worked with a college roommate to produce a freely available program called "RogueRemover", a utility which specialized in fighting against a type of infection known as "rogues", which scam computer users into giving away their credit card information through fake anti-virus software.

[18] In January 2016, Malwarebytes unveiled advanced anti-ransomware package Endpoint Security,[19] and announced that it had raised $50 million in investment from Fidelity Management and Research Company.

[11] In June, Malwarebytes announced a strong growth in sales of over 75 percent in the first quarter of the year compared to 2015, with billings surpassing $100 million.

[20] In September, Proofpoint, Inc. CEO Gary Steele joined the company's board of directors, with Kleczynski citing his "deep expertise in the security software industry, and his proven ability [at] increasing sales revenue" as the main reasons for his appointment.

[21] In February 2017 the company acquired Saferbytes, an Italian security start-up specialized in anti-malware, anti-exploit, anti-rootkit, cloud AV, and sandbox technologies.

[22] In November 2019, the company joined forces with NortonLifeLock and Kaspersky, along with the Electronic Frontier Foundation and non-profits including the National Network to End Domestic Violence and Operation Safe Escape to form the Coalition Against Stalkerware.

[23] In January 2021, Malwarebytes was targeted by the same nation state actor implicated in the SolarWinds attack and suffered a limited access breach.

[27] In May 2021, Malwarebytes announced a collaboration with Digitunity to deliver cyberprotection to vulnerable communities underserved by technology access, expanding its portfolio of social impact work.

[35] The company also launched Malwarebytes Anti-Exploit in the same year, which shields selected applications from attacks by "exploit mitigation to protect vulnerable programs".

The free version stops exploits in browsers and Java, whilst the paid product adds protection for a wider range of software applications.

Due to Apple's security restrictions, Malwarebytes for iOS can not remove malware, but does provide basic web protection and spam blocking.

[6] The software license[45] requires arbitration "in the county where you reside", forbids class action suits, reverse engineering and sharing, and limits warranties and liability.

Malwarebytes' privacy policy[46] lists many types of information they collect and store, including, amongst other things, software running on a user's computer ("programs installed or in use"), "name, email address, mailing address, or phone number... company name, company size, business type... Internet protocol (IP) addresses, browser type, Internet service provider (ISP), referring/exit pages, the files viewed on our site ... operating system, date/time stamp, and/or clickstream data ... type of device you use, operating system version, and the unique device identifier... language... 32- or 64-bit... Information from the Windows Security/Action Center, including security settings and programs installed or in use... license... the number of seats being managed by that installation of the console[,] Endpoint domain information... organization to which the IP address is licensed, if any".