After retiring from playing, Duff coached Burnley's under-18 squad in 2016 before becoming head coach of the under-23 squad in 2017. He also worked with Burnley's first-team, travelling with the squad to several
UEFA Europa League matches in 2018. His first win was a 6–2 victory over
Arsenal's
under-21s in the
EFL Trophy. In his second season, Duff won the
League Two Manager of the Month award for September 2019 and February 2020. He won the award in February after Cheltenham achieved 18 points from 21, with the club sitting in fifth place and four points from automatic promotion. They led City 1–0 before conceding three goals in the final 10 minutes. Duff was named the
League Two Manager of the Season and Cheltenham finished the season as champions. Duff then led the club to their highest-ever finish in the Football League at the end of the
2021–22 season; a 15th-placed finish in
League One. In June 2022, after nearly four years at the club, Duff informed Cheltenham that he wished to depart for new opportunities.
Barnsley On 15 June 2022, Duff was appointed head coach of recently relegated League One side
Barnsley on a three-year deal. Duff won the
League One Manager of the Month award for November 2022, with Barnsley winning both of their two league games during the month. He won the award for a second consecutive month after ten points from four matches saw the club rise to fourth in the table. Duff won the award again in February 2023, with Barnsley having gained 16 points from six matches and remained unbeaten throughout the month. He led the club to the
play-off final at the end of the season, losing 1–0 to
Sheffield Wednesday in extra time.
Swansea City Duff was named head coach of
Championship club
Swansea City on 22 June 2023. He signed a three-year deal, with Barnsley being paid compensation. His debut on 5 August was a 1–1 draw at home to
Birmingham City; Tom Coleman of
Walesonline praised him for using different tactics to predecessor
Russell Martin. Swansea took three points from a seven-game winless run at the start of the season before defeating
Sheffield Wednesday 3–0 at the
Swansea.com Stadium on 23 September; this was the first of four wins in a row, followed by one win in eight for the rest of his tenure. The club dismissed Duff on 4 December 2023.
Huddersfield Town On 13 May 2024, Duff was appointed head coach of newly relegated
EFL League One club
Huddersfield Town on a three-year contract. His team went unbeaten for 16 games between October and January, rising from 15th to 4th.
Wycombe Wanderers On 18 September 2025, Duff was appointed as the head coach of
Wycombe Wanderers, who were 19th in
EFL League One after the dismissal of
Mike Dodds. ==Personal life==