Skuse began the 2006–07 season in the starting eleven, but was dropped after being substituted off at half-time against Blackpool on 19 August. His next start came nearly two months later, setting off a run of 27 starts in 29 league matches. The club finished the season in second place, earning their first participation in the second-tier in eight seasons. Skuse made 42 appearances in the league, as well as 5 in the FA Cup, in which the Robins were eliminated in a fourth-round replay by Middlesbrough.