Atkins' first major exposure as a drummer was with John Lydon's post-Sex Pistols band, Public Image Ltd. He joined in 1979, just in time to contribute to the song "Bad Baby" on the album Metal Box. Atkins' first live show with PiL was recorded and released as a live album Paris au Printemps and his first year with the band included appearances on The John Peel Sessions for the BBC, American Bandstand and the BBC's live Old Grey Whistle Test.
In 1980, Atkins left Public Image Ltd to concentrate on his band Brian Brain with Pete Jones (who also played with Public Image Ltd in 1982 and 1983) on bass (in 1983 replaced by original Go-Gos' bassist Margot Olavarria) and Bobby Surgeoner on guitar (later replaced by Olavarria's husband, Geoff Smyth). Brian Brain released six singles and one LP (Unexpected Noises) on Secret Records, and continued to release singles and LPs on Atkins' own Plaid Records throughout the 1980s. The band had a minor indie chart hit in 1980 with "They've Got Me in the Bottle" (#39), and club hits with the singles "Jive Jive" (1981) and "Funky Zoo" (1982).
Atkins rejoined Public Image Ltd in 1981 to contribute to The Flowers of Romance and, later, produced and co-wrote the album This Is What You Want... This Is What You Get. Atkins eventually left PiL for the last time in 1985.
After leaving Public Image Ltd, Atkins revived his Brian Brain project and recorded an EP at Planet Sound Studios in New York for his own, short-lived label Plaid Records, which was released in July 1985. Throughout the late 1980s, the 1990s and early 2000s, Atkins performed with many bands, including Nine Inch Nails (appearing in the video for "Head Like A Hole"), as well as Ministry. The dual-drumming of Atkins and Bill Rieflin is captured on the live Ministry album/video In Case You Didn't Feel Like Showing Up. Atkins later joined Killing Joke, performing on 1990s Extremities, Dirt, and Other Repressed Emotions. He also managed the band for that time, and designed their live show scenery and some merchandise.
Atkins formed his industrial supergroup, Pigface, during a Ministry tour in 1989–1990. Atkins also went on to form Murder, Inc., a new band featuring Geordie Walker, Paul Raven and Chris Connelly, in 1992. During this time, he played with the Revolting Cocks and is credited alongside Chris Vrenna in Nine Inch Nails for performing extra drums on "Wish" and "Gave Up," tracks two and six of the Broken EP (as well as the aforementioned "Head Like A Hole").
In between creating albums and touring with Pigface he also began The Damage Manual, which combined the bass and percussion feel of early PiL bass player Jah Wobble with Atkins' signature beats and production. Geordie Walker from Killing Joke and Chris Connelly were also part of the project.
Atkins later produced and released a collaborative album with Skinny Puppy's Nivek Ogre, the latter's first project outside of Skinny Puppy, under the moniker Rx. The resulting album was entitled Bedside Toxicology.
Between 2000 and 2002 he released four albums as Opium Jukebox featuring instrumental cover tunes done in a Bhangra style.
In October 2006, Atkins visited Beijing to discover the emerging Chinese music scene. During his stay, Atkins recorded and signed a handful of Chinese bands to Invisible Records and recorded material for a new Pigface album.
Atkins has taught at Columbia College in Chicago where he instructed the course "The Business of Touring". He is also an active guest lecturer, speaking at such institutions as the University of Southern California, the Midi School in Beijing and Lebanon Valley College in Annville, Pennsylvania. Atkins has since become an instructor at the Madison Media Institute in Madison, Wisconsin. Atkins has announced plans to take his lecturing further by eventually opening a school of his own. He is also a department chairman for a music business program he designed at SAE Chicago.
Atkins has held a number of seminars at Tech Music Schools (Drumtech, Vocaltech, Guitar-X and Keyboardtech) in London, with more planned for the future.
Atkins has written what he calls, "the first real book on touring". The book Tour:Smart, featured contributions from Henry Rollins, Cynthia Plastercaster, The Enigma, the Suicide Girls, Zim Zum (formerly of Marilyn Manson), Kevin Lyman, Curse Mackey and various other managers, journalists, venues, agents, sponsors, and radio personalities.
Atkins was on the tenth annual Independent Music Awards judging panel, and was also a judge for the seventh annual season of Independent Music Awards to support independent artists.
Starting in 2015, Atkins has written and performed several podcast stories for The Martin Atkins Minute, included with the NPR All Songs Considered podcast.