Jones moved to the CFL in 2002, after being an Ast. Coach for Arena LeagueLas Vegas in the spring and summer, after being named the new defensive line coach of the Montreal Alouettes helping Montreal win the 90th Grey Cup. He remained there until 2007. In 2008, he was named defensive coordinator of the Calgary Stampeders, which won the 96th Grey Cup, and was promoted to Assistant Coach in 2010. He later joined the Toronto Argonauts as Defensive Coordinator and was part of the team that won the 100th Grey Cup.
Jones was named head coach of the Edmonton Eskimos in November 2013. After a 12-6 2014 season, he was nominated for CFL Coach of the Year. Jones was nominated as the West representative for coach of the year in 2015 after winning 14 of the 18 regular season games. The East representative and winner was former Eskimos assistant coach Rick Campbell. Jones' Eskimos were victorious over the Ottawa Redblacks in the 103rd Grey Cup game. Following the season the divisional rival Saskatchewan Roughriders were given permission by GM Ed Hervey to entering into negotiations to fill their vacant head coaching position.
Saskatchewan Roughriders
On December 7, 2015, a mere week after winning the 2015 Grey Cup, it was announced that Jones would be the new general manager and head coach of the Saskatchewan Roughriders. After a disappointing 3-15 season in 2015 Jones took over in 2016 and things got off to poor start, as the team won only one of their first 11 games. However, down the stretch they would win four of the remaining seven games and finish with a record of 5-13. 2017 saw the Riders return to being a competitive team, as the club qualified for the playoffs for the first time since 2014. After defeating the Ottawa Redblacks in a crossover playoff game the Riders were bested by the Toronto Argonauts who would go on to win the 105th Grey Cup. Following the season the Riders extended Jones' contract through the 2019 CFL season. Jones and the Riders continued to improve in the 2018 season, accumulating 12 wins, but in the playoffs they were defeated by the Winnipeg Blue Bombers. On January 8, 2019 Jones and the Riders agreed to a new two-year contract extension.
Cleveland Browns
On January 15, 2019, one week after signing a contract extension with the Roughriders, Jones resigned from the Roughriders to take a job with the Cleveland Browns as their Senior Defensive Specialist.
Personal life
Jones has a son from his first marriage and two daughters with his second wife. He and his family reside in South Pittsburg, Tennessee. He also has a dog and 2 cats.