Isbell was born in Green Hill, Alabama, two miles from the Alabama/Tennessee state line, the son of interior designer mother Angela Hill Barnett and house painter Mike Isbell. Isbell's mother was only 17 years old (and his father 19 years old) when he was born and is the subject of a song, "Children of Children". Isbell's parents divorced, and he has two much younger half-siblings, Chantry Barnett and Emily Isbell. Isbell grew up in rural North Alabama.

After working as a songwriter, in 2001 at the age of 22, Isbell joined the rock band Drive-By Truckers while they toured in support of their album Southern Rock Opera. The band operates out of Athens, Georgia, where Isbell lived while with the band. Patterson Hood recalls that he met Isbell through Dick Cooper, a mutual friend from Muscle Shoals. Hood already knew Shonna Tucker and invited Isbell to join Drive-by Truckers after he sat in with the group at an acoustic house party when guitarist Rob Malone didn't show up.  Isbell recorded and contributed many songs to Drive-by Truckers for their next three albums, 2003's Decoration Day, 2004's The Dirty South, and 2006's A Blessing and a Curse. The title track of Decoration Day was revealed by Isbell in the 2014 Live from Lincoln Center concert to be a true story about his family members.  For most of his time as a band member, Isbell was married to Shonna Tucker, who joined the band after Isbell as a bassist. The two were part of the band's documentary, The Secret to a Happy Ending. The two later divorced.  On April 5, 2007, Isbell announced that he was no longer a member of Drive-By Truckers. The following day, Patterson Hood confirmed the break on the band's official site. In his letter to the fans, Hood described the parting of ways as "amicable" and expressed the hope that fans would continue to support Drive-By Truckers as well as Jason's solo efforts. Isbell had been with the Drive-By Truckers for six years.  On June 15, 2014, Isbell teamed with Hood and Mike Cooley for a benefit at the Shoals Theater in Florence, Alabama. The sold-out acoustic performance was the first time Isbell had performed with his former bandmates since they split in 2007. In August 2015, Hood joined Isbell onstage and played a couple of Drive-By Truckers songs together in Hood's new adopted hometown of Portland, Oregon.

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