Solo work and band projects: 1984–present
During his time in Faith No More, Patton continued to work with Mr. Bungle. His success in mainstream rock and metal ultimately helped secure Mr. Bungle a record deal with Warner Bros. The band released a self-titled album (produced by John Zorn) in 1991, and the experimental Disco Volante in 1995. Their final album, California, was released in 1999. The band ceased being active following the 1999–2000 tour in support of the California record, although their disbandment was only officially confirmed in November 2004. Mr. Bungle reunited in 2019 with three original members (Patton, Dunn and Spruance) plus drummer Dave Lombardo and guitarist Scott Ian to re-record its first demo from 1986 The Raging Wrath of the Easter Bunny; the album was released on October 30, 2020.
Patton's other projects included two solo albums on the Composer Series of John Zorn's Tzadik label, (Adult Themes for Voice in 1996 and Pranzo Oltranzista in 1997). He is a member of Hemophiliac, in which he performs vocal effects along with John Zorn on saxophone and Ikue Mori on laptop electronics. This group is billed as "improvisational music from the outer reaches of madness". He has also guested on Painkiller and Naked City recordings. He has appeared on other Tzadik releases with Zorn and others, notably as part of the "Moonchild Trio" alongside Joey Baron and Trevor Dunn, named after Zorn's 2006 album on which the trio first appeared, Moonchild: Songs Without Words.
In 1998, Patton formed the metal supergroup Fantômas with guitarist Buzz Osborne (of The Melvins), bassist Trevor Dunn (of Mr. Bungle), and drummer Dave Lombardo (of Slayer). They have released four studio albums. In 1999, Patton collaborated with Japanese experimental musician Merzbow on the album She, released under the name Maldoror.
In 1999, Patton met former The Jesus Lizard guitarist Duane Denison at a Mr. Bungle concert in Nashville, and the two subsequently formed the band Tomahawk. Tomahawk's straightforward rock sound has often been compared to Album of the Year/King for a Day era Faith No More.
In 2001, he contributed vocals to Chino Moreno's group Team Sleep and released the album Music to Make Love to Your Old Lady By with the group Lovage, a collaborative project consisting of Patton, Dan the Automator, Jennifer Charles, and Kid Koala.
Patton performed vocals for Dillinger Escape Plan's 2002 EP, Irony Is a Dead Scene. That year, he joined violinist Eyvind Kang and his ensemble Playground to play the piece Virginal Co Ordinates at the AngelicA International Festival of Music in Bologna. The performance would be released as an album in 2003.
In 2004, Patton worked with Björk and the beat boxer Rahzel on the album Medúlla. That same year, Patton released the album Romances with Kaada and contributed vocals to the album White People by Handsome Boy Modeling School (Dan the Automator and Prince Paul). In 2005, Patton collaborated with hip hop DJ trio and turntablists The X-Ecutioners to release the album General Patton vs. The X-Ecutioners.
In February 2006, Mike Patton performed an operatic piece composed by Eyvind Kang, based on the 1582 work Cantus Circaeus by Giordano Bruno, at Teatro Comunale di Modena in Modena, Italy. Patton sang alongside vocalist Jessika Kenney, and was accompanied by the Modern Brass Ensemble, Bologna Chamber Choir, and Alberto Capelli and Walter Zanetti on electric and acoustic guitars. The singer remarked that it was extremely challenging to project the voice without a microphone. This performance was later released as the record Athlantis in July 2007, through Ipecac Recordings.
Patton's Peeping Tom album was released on May 30, 2006, on his own Ipecac label. The set was pieced together by swapping song files through the mail with collaborators like Dan the Automator, Rahzel, Norah Jones, Kool Keith, Massive Attack, Odd Nosdam, Amon Tobin, Jel, Doseone, Bebel Gilberto, Kid Koala, and Dub Trio.
In 2008, he performed vocals on the track "Lost Weekend" by The Qemists. In December 2008, along with Melvins, Patton co-curated an edition of the All Tomorrow's Parties Nightmare Before Christmas festival. Patton chose half of the lineup and performed the album The Director's Cut in its entirety with Fantômas. Patton also appeared as Rikki Kixx in the Adult Swim show Metalocalypse in a special 2 part episode on August 24.
In June 2009, Mike Patton and Fred Frith performed in Queen Elizabeth Hall, London, England as part of that year's Meltdown Festival.
On May 4, 2010, Mondo Cane, where Patton worked live with a 30-piece orchestra, was released by Ipecac Recordings. The album was co-produced and arranged by Daniele Luppi. Recorded in 2007 at a series of European performances including an outdoor concert in a Northern Italian piazza, the CD features traditional Italian pop songs of the 1950s and 1960s as well as a rendition of Ennio Morricone's "Deep Down".
On June 18, 2010, Patton performed the 1965 work Laborintus II by classical composer Luciano Berio in Amsterdam, along with the orchestra Ictus Ensemble and vocal group Nederlands Kamerkoor. This show would be released as an album on July 10, 2012. On October 8, 2016, Patton and Ictus Ensemble played this piece in Krakow, Poland, preceded by a performance of the album Virginal Co Ordinates the previous day, alongside its creator Eyvind Kang.
Patton is a member of the supergroup Nevermen, alongside Tunde Adebimpe of TV on the Radio and rapper Doseone (with whom Patton had previously collaborated on the Peeping Tom side project). In 2016, the group released an eponymous debut album on Patton's Ipecac label.
In August 2017, Patton released an album with the band Dead Cross, a supergroup that includes Slayer and Fantômas drummer Dave Lombardo and Retox members Michael Crain and Justin Pearson.
On December 27, 2017, Patton performed his collaborative EP, Irony Is a Dead Scene, as well as a cover of Faith No More's "Malpractice," with the Dillinger Escape Plan live at the band's first of three final shows at Terminal 5 in New York City.
In May 2018, Patton performed two concerts entitled Forgotten Songs in Modena, Italy, with the American pianist Uri Caine. The setlists of the concerts varied and included songs from Olivier Messiaen, Elton John, Slayer, Violeta Parra, George Gurdjieff, and many others. They also performed a new song called "Chansons D'amour" from an album Patton would later release with French musician Jean-Claude Vannier, Corpse Flower of September 2019. The shows were recorded, but it is not certain if the material will get a release.
On January 25, 2020, Patton joined Laurie Anderson and Rubin Kodheli at the SFJAZZ Center for a performance based on the 16th century military manual Quanjing Jieyao Pian by Qi Jiguang.
In September 2021, Faith No More was scheduled to play shows. However, the dates were cancelled due to Patton citing mental health reasons.
On September 16, 2025, after teasers on the respective artist's social media, Mike Patton and The Avett Brothers announced their collaborative project 'AVTT/PTTN', which would release on November 14th, 2025 via Thirty Tigers in association with Ramseur Records and Ipepac Recordings. Subsequently they would announce tour dates for 2026 and would appear on The Tonight Show Starring Jimmy Fallon and CBS Mornings to promote the collaboration.