Theodore was The Mars Volta's drummer from 2001 to 2006. On July 30, 2006, it was announced that Jon Theodore would be permanently replaced. He was quoted in Modern Drummer: "It was long overdue and unquestionably the best thing for everyone involved. We had a great run of things, made some decent records, blew it up for a minute, and had some really great times. But the life ran out of it. I'm currently working on some pretty sweet tunes for a new project. The details will follow once it takes shape." In 2012, Mars Volta bassist Juan Alderete stated, "I love Jon, and I do keep in touch with him. Jon was unhappy and when someone is unhappy, someone has to pull the trigger; and its Omar's band so he did just that. They had to let him go because he wasn't into it as much as they wanted him to be." Theodore has also completed a collaboration with Zack de la Rocha of Rage Against the Machine entitled One Day as a Lion. Their first EP was released on July 22 of 2008 In January 2012, he joined Giraffe Tongue Orchestra, replacing fellow former Mars Volta drummer Thomas Pridgen. He recently played as Dam Funk's touring drummer during his Fall 2012 US Tour. A press release from the band Queens of the Stone Age revealed that Theodore will contribute drums on their upcoming album "...Like Clockwork". He played on one track on the album, the title track. It was the first Queens album to reach number one on the "Billboard" 200. It also reached number two on the UK Albums Chart and was nominated for three Grammy Awards, including Best Rock Album. Following the release of the album in 2013, he has gone on to become the permanent drummer of Queens of the Stone Age. In 2018, Theodore performed drums on certain sections of the score for the video game Red Dead Redemption 2. His Queens of the Stone Age bandmates Joshua Homme and Michael Shuman also are featured on the score. Theodore draws inspiration from many different forms of music but those most prevalent in his playing are jazz, fusion, and rock. He has also touched upon another factor which adds to his individual style - ""Then there's a whole bunch of stuff from Haiti because my dad's Haitian. My favorite Haitian drummer is this guy called Azor... ... The Haitian music that moves me has the drumming from the voodoo rituals. It moves me because the patterns are connected to different spirits; it's a spiritual thing that is interconnected with dancing, sacrifice and devotion.