After his playing career ended, Lindgren worked at the University of Redlands as the football team's quarterbacks coach in 2005. He joined the coaching staff at Northern Arizona in 2006 as a receivers coach, working his way up to offensive coordinator in 2009. He left Northern Arizona to accept the offensive coordinator position at San Jose State in 2012.[4] He was a finalist for the head coaching job at his alma mater Idaho in 2012, but the job ultimately went to Paul Petrino.[5][6]
Colorado
After San Jose State head coach Mike MacIntyre was named the new head coach at Colorado, Lindgren joined him as his offensive coordinator, the same position he held under him at San Jose State.[7][8] He was shifted to co-offensive coordinator in 2016 following the hire of Darrin Chiaverini, sharing coordinator duties with Chiaverini.[9]
Oregon State
Lindgren was hired to be the offensive coordinator and quarterbacks coach at Oregon State in 2018 under new head coach Jonathan Smith.[10] It was reported in December 2019 that Lindgren was offered the offensive coordinator position at Arizona State, but he turned down the offer.[11]