It was on tour with Califone that he befriended the members of Modest Mouse and The Shins, who took an interest in Fruit Bats and made an introduction to the record label Sub Pop.

[11][12] Johnson left the band in 2011 due to scheduling conflicts with Fruit Bats, and went on to appear on several tracks on their fourth studio album, Port of Morrow.

[15] Later that year he worked on director Jesse Peretz’s feature Our Idiot Brother, starring Paul Rudd, which premiered at the Sundance Film Festival in 2011.

Johnson co-scored the film with Nathan Larson, and also wrote and produced three original songs for the soundtrack, as well as contributing a cover of "Tie a Yellow Ribbon Round the Ole Oak Tree."

In 2013 Johnson collaborated with Vetiver front man Andy Cabic on scores for two critically lauded Sundance features - one for the dramedy Smashed and the other for the documentary After Tiller.

[16] In 2012 Johnson collaborated with Andy Cabic of Vetiver on the music for the critically lauded Sundance feature Smashed, a score which landed on the Academy Awards’ shortlist for that year.

[17] In 2016 Johnson scored director Rod Blackhurst’s feature debut Here Alone, which won the Tribeca Film Festival’s audience award.

Johnson has occasionally appeared as an actor, most notably a cameo as a Grateful Dead cover band member in Jean-Marc Vallée’s 2014 drama Wild.

He also provided voices for various characters in the cartoon pilot E Coli High which premiered on IFC Selects,[18] as well as the voiceover for TurboTax’s Super Bowl Ad in 2021.

Produced and curated by Johnson, the festival has frequently featured not only sets from Fruit Bats, but also acts such as Jonathan Wilson, Hand Habits, Robyn Hitchcock, Lee Fields, Real Estate, Love, Shannon and the Clams, Silver Apples, Tara Jane O'Neil, Bob Weir, and many more.

[20] In November 2012 at San Francisco’s Warfield Theatre, Johnson performed Van Morrison’s songs from The Last Waltz in a recreation of The Band’s 1976 farewell concert of the same name.

[22] In 2018, Johnson curated and produced a set at Newport Folk Festival called Beneath the Sacred Mountain: A Cosmic American Revue with support from The Spacebomb House Band, Phil Cook, Josh Kaufman, Matthew E. White, James Mercer (The Shins), The Watson Twins, Laura Veirs, Hiss Golden Messenger, Bedouine, and Lucius.