After the departure of Ron Atkinson, Francis took over as manager of Sheffield Wednesday with popular support from club and supporters. He guided Wednesday to an excellent third-place finish in 1992. The following year, Wednesday reached the FA Cup and League Cup finals, losing both to Arsenal, the former after a replay. In 1994, Francis finally retired as a player, shortly before his 40th birthday. He was sacked as manager a year later after Wednesday finished 13th in the Premiership.