Skuse began the 2008–09 season in the team for the first time since the club's promotion to the Championship, and started the club's first nine games, playing both in midfield and at right-back. After that, Skuse was out injured for nearly two months. He returned to enter as a half-time substitute for Jamie McCombe against Nottingham Forest, but missed the next three games, before returning again on 8 December against Swansea City. His first goal in the Championship came against Norwich on 7 February, and he scored again two weeks later against Reading. In total, Skuse made 29 starts in the league that season, as well as starting all four cup games, as the club finished in 10th.