Johnston began performing with Uncle Tupelo in the fall of 1992 during the "Arkansas Traveler Review tour" during which Uncle Tupelo was the opening act for a bill including The Band, Taj Mahal, and headliner, Michelle Shocked. Although the tour fell apart after just a few shows, Johnston continued to play with Uncle Tupelo occasionally at first, and then as a regular part of the band appearing on the group's final studio album, Anodyne.
Johnston was offered a position in The Gourds and immediately accepted it after sitting in with the band at their South by Southwest showcase. After years of performing mainly as a sideman for great songwriters (Farrar, Tweedy, Shocked, and Irwin), Johnston at last felt himself to be a contributing member of the band. "This is more mine than anything I've ever been involved with," Johnston stated, "I have a voice in this band. With Tupelo, it was like, 'Wow, I'm in Uncle Tupelo,' you know? But I didn't have much input. Here, I finally found a group of guys who listen to me, we communicate on a level I haven't before." By the time of his second recording with the band, Bolsa de Agua, Johnston had found his voice contributing the tracks, "Jesus Christ (with Signs Following)" and "O Rings". Johnston has continued to remain active with The Gourds, whose most recent release is 2011'sOld Mad Joy. On October 7, 2014 Johnston released a solo album, "Dismantling Paradise".