On January 3, 2018, Jones was announced as the new offensive coordinator for the Montreal Alouettes for the 2018 CFL season. On June 8, 2019, less than a week before the start of the 2019 season, the Alouettes announced they had parted ways with Mike Sherman and promoted Jones to the role of head coach. Despite being thrust into the role six days before the start of the regular season, Jones and the Alouettes surpassed expectations and finished with a 10–8 record and in second place in the East Division. At the conclusion of the season, he was signed to a three-year contract extension to continue as the team's head coach and offensive coordinator.