Skuse started the first eight games of the 2011–12 season, but was left out of the squad for the next two, which proved to be the final matches for Keith Millen in charge. The club hired new manager Derek McInnes from St Johnstone, who played Skuse in the full-back position on the right hand side. After picking up another toe injury against Crystal Palace on 14 February, Skuse missed the next month and a half. Upon his return, Skuse was returned to the midfield, and winter transfer Ricky Foster was used at right-back. Skuse scored the first goal in a 2–0 win at home to Barnsley on 21 April, securing the club's Championship status for next season. He also scored in a 1–1 draw with West Ham a few days earlier, and finished the season with two goals in 36 starts, as the club finished in 20th, nine points clear of relegation.