After Led Zeppelin
Led Zeppelin dissolved in 1980 with the death of John Bonham. "At the time that John died, I had just moved to Devon to bring up my family", Jones said. "So, after the split, I was completely out of everything. And I must say I didn't miss it."
Jones subsequently collaborated with artists including Diamanda Galás, R.E.M., Jars of Clay, Heart, Ben E. King, Peter Gabriel, Foo Fighters, Lenny Kravitz, Cinderella, The Mission, La Fura dels Baus, the Harp Consort, Brian Eno, the Butthole Surfers, and Uncle Earl.
He appeared on sessions and videos for Paul McCartney and was involved in the soundtrack of the film Give My Regards to Broad Street. In 1985, Jones was asked by director Michael Winner to provide the soundtrack for the film Scream for Help, with Jimmy Page appearing on two tracks. Jones provides vocals for two of the songs. He recorded and toured with singer Diamanda Galás on her 1994 album, The Sporting Life (co-credited to John Paul Jones). In 1985, Jones joined Page and Plant for the Live Aid concert, with Phil Collins and Tony Thompson on drums. The former members again re-formed for the Atlantic Records 40th Anniversary concert on 14 May 1988. Page, Plant and Jones, with John Bonham's son Jason, closed the event. In 1992, Jones arranged the orchestration on the R.E.M. album Automatic for the People.
In 1995, the band Heart released a live acoustic album called The Road Home. It was produced by Jones, and featured him playing several instruments. Also in 1995, Andrew Lawrence-King's Harp Consort released a set of three Spanish language songs in 17th-century style of Jones's own composition, accompanied by baroque instruments including harps, chitarrone, guitars, lirone, viola da gamba and percussion (this 10-minute CD, titled Amores Pasados, was coupled with The Harp Consort's debut record, Luz y Norte).
Zooma, his debut solo album, was released in September 1999 on Robert Fripp's DGM label and followed up in 2001 by The Thunderthief. Both albums were accompanied by tours, in which he played with Nick Beggs (Chapman Stick) and Terl Bryant (drums).
In 2004, he toured as part of the group Mutual Admiration Society, along with Glen Phillips (the front man for the band Toad the Wet Sprocket) and the members of the band Nickel Creek.
Jones plays on two tracks on the Foo Fighters' album In Your Honor. He plays mandolin on "Another Round" and piano on "Miracle", both of which are on the acoustic disc. The band's frontman Dave Grohl (a big Led Zeppelin fan) has described Jones' guest appearance as the "second greatest thing to happen to me in my life".
He has also branched out as a record producer, having produced such albums as the Mission's album Children, the Datsuns' second album Outta Sight, Outta Mind (2004) and Uncle Earl's Waterloo, Tennessee album of Old-time music, released in March 2007 on Rounder Records.
In May 2007, he accompanied Robyn Hitchcock and Ruby Wright in performing the song "Gigolo Aunt" at a tribute for Pink Floyd founder Syd Barrett in London, which he did on mandolin.
He played at Bonnaroo 2007 in a collaboration with Ben Harper and the Roots' drummer Questlove as part of the festival's all-star Super-Jam, which is the festival's annual tradition of bringing together famous, world-class musicians to jam on stage for a few hours.
Jones appeared and played mandolin with Gillian Welch during the festival during the song "Look at Miss Ohio" and a cover of the Johnny Cash song "Jackson". He also appeared during the set of Ben Harper & the Innocent Criminals where they played a cover of "Dazed and Confused". Jones then closed Gov't Mule's first set, playing part of "Moby Dick" and then "Livin Lovin Maid" on bass, then proceeded to play keyboards on the songs "Since I've Been Loving You" and "No Quarter". Jones also performed on mandolin with the all-female bluegrass group Uncle Earl, whose album he had produced in 2007.
Mandolin-slinging Jones jammed on Led Zeppelin's "Whole Lotta Love" with Winnipeg's energetic Duhks at April 2007's MerleFest in North Carolina.
Jones played in the Led Zeppelin reunion show at London's O2 Arena on 10 December 2007 with the other remaining members of Led Zeppelin as part of a tribute to Ahmet Ertegun.
In 2008, Jones produced Nickel Creek singer-fiddler Sara Watkins' debut solo album. As previously mentioned, Jones toured with Watkins, Glen Phillips, and the rest of Nickel Creek in late 2004 in a collaboration entitled Mutual Admiration Society.
On 10 February 2008, Jones appeared with the Foo Fighters on the Grammy Awards conducting the orchestral part to the song "The Pretender". On 7 June 2008, Jones and Jimmy Page appeared with the Foo Fighters to close out the band's concert at Wembley Stadium. Jones performed with Sonic Youth and Takehisa Kosugi, providing the stage music for Merce Cunningham's Nearly 90, which ran 16–19 April 2009 at the Brooklyn Academy of Music.
In 2009–2010 he was part of a supergroup with Dave Grohl and Queens of the Stone Age frontman Josh Homme named Them Crooked Vultures. The trio played their first show together on 9 August 2009 at the Metro in Chicago, and their first album was released on 17 November 2009.
In February and March 2011, he appeared in the onstage band in Mark-Anthony Turnage's opera Anna Nicole, about the Playboy model Anna Nicole Smith, at the Royal Opera House, Covent Garden, in London. In August 2011, he appeared at Reading and Leeds Festivals to play alongside Seasick Steve. On 16 September 2012, Jones appeared at the Sunflower Jam charity concert at the Royal Albert Hall, London, performing alongside guitarist Brian May of Queen, drummer Ian Paice of Deep Purple, and vocalists Bruce Dickinson of Iron Maiden and Alice Cooper.
In November 2012, Jones toured the UK with the Norwegian avant-garde/improvisational band Supersilent. On 6 December 2012, Jones performed on bass, guitar and mandolin with Robyn Hitchcock as 'Biscotti' at Cecil Sharp House, London.
On 30 April 2013, Jones appeared live on the BBC TV Show Later... with Jools Holland, playing bass for Seasick Steve on "Down on the Farm" from Seasick Steve's new album Hubcap Music. On 1 May 2013, Jones appeared with Seasick Steve at a concert at the Roundhouse in Camden, London. Introduced by Seasick Steve as a member "of the best rock band ever", Jones played bass, mandolin, and steel guitar, and provided vocals.
On Saturday 29 June 2013, Jones played guitar whilst appearing with Rokia Traoré, who opened the Pyramid Stage that morning at Glastonbury 2013. He also supported Seasick Steve on the West Holt's stage at the same festival.
During November 2013, Jones joined a seven-day tour of the Southeast US, playing mandolin with the Dave Rawlings Machine. The Atlanta show (21 November 2013) included a rendition Led Zeppelin's "Going to California." Jones also toured with the Dave Rawlings Machine in autumn 2014. On 5 and 6 September 2015, Jones, along with Queen drummer Roger Taylor, joined Foo Fighters on stage in Milton Keynes to perform a cover of Queen's "Under Pressure," with Taylor Hawkins and Dave Grohl singing. Stepping outside his normal genre, he composed three lute songs for the 2015 album Amores Pasados by John Potter, Anna Maria Friman, Ariel Abramovich and Jacob Herringman.
In 2017, Jones formed a trio, the "Tres Coyotes" with the Finnish composer, Magnus Lindberg and the Finnish cellist, Anssi Karttunen, they have performed in Helsinki (Savoy Theatre 2017), Torino (Torino Jazz Festival 2019) and Strasbourg (Festival Musica 2022). In 2019 he formed a duo, called the "Sons of Chipotle" with Anssi Karttunen. The group premiered with a tour in Asia in Seoul at Place Vib and in Tokyo at the Pit Inn in Tokyo, Japan in September of that year. For the Tokyo shows they were joined by musicians Jim O'Rourke and Otomo Yoshihide The band's first scheduled US date at the Big Ears Festival in Knoxville, Tennessee was cancelled in March 2020, due to the COVID-19 outbreak and finally took place at the Big Ears in 2024.
In 2025, Jones appeared in the musical documentary Becoming Led Zeppelin, directed by Bernard MacMahon and produced by Allison McGourty. It was the first time the band's members had agreed to participate in a biographical documentary.