Wilson completed a solo album titled, Frankie Ray in 2007. The record was never officially released. Since, Wilson has recorded the full length album, Gentle Spirit, which was released on Bella Union on August 8, 2011 in the UK & Europe and on September 13, 2011 in the US. The album debuted at number 15 on the UK Indie Chart and was awarded the #4 spot on Mojo's 2011 Best Albums of the Year list. Gentle Spirit features many special guests including Barry Goldberg, Chris Robinson, Gary Louris, Andy Cabic, Otto Hauser, Josh Grange, Gary Mallaber, Z Berg, Adam McDougall, Johnathan Rice, among others. Jonathan was named Uncut Magazine's 2011 "New Artist of the Year".
Wilson was invited by Roy Harper as a special guest at Royal Festival Hall in November 2011 as part of Harper's sold out 70th Birthday celebration. Wilson will tour with Wilco in the Fall of 2011 for 15 shows across the UK & Europe. In July 2011 Wilson performed and collaborated with Jackson Browne and Dawes on several shows throughout Spain. Wilson performed at the 2011 benefit concert for Musicians United for Safe Energy (MUSE) at Shoreline Amphitheater joining Crosby, Stills & Nash, Jackson Browne, Bonnie Raitt, John Hall, The Doobie Brothers, Jason Mraz, Tom Morello, Kitaro, Sweet Honey In The Rock and others. Wilson was joined onstage by Jackson Browne and Graham Nash to perform his song "Gentle Spirit". Wilson also joined Crosby, Stills & Nash, Jackson Browne, Bonnie Raitt and others for the concert's finale, "Teach Your Children". In 2011, Wilson collaborated with Graham Nash on a cover of George Harrison's "Isn't It A Pity". In 2010 and 2011, Wilson collaborated with Erykah Badu in the studio on several songs, only one of which was officially released. Wilson also appeared as a special guest with Erykah Badu at her 2011 Coachella performance.