After signing a new deal at City in summer 2009, Skuse scored his first goal of the 2009–10 season in a 1–1 home draw with Peterborough. Skuse's second of the campaign, and sixth for Bristol City, came away at Leicester City, to help his team to a 3–1 victory. He wound up making a career-high 43 appearances in the league, and started every match bar one after September, playing alongside Marvin Elliott in midfield. Skuse was voted the club's player of the season for the 2009–10 season, as well as young player of the year. At the time, only Matt Hill had won both awards in the same season. After the season, new manager Steve Coppell offered Skuse a new extended contract until 2013, which he signed. He also started all four cup games for the club that season, including an FA Cup third-round replay defeat to rivals Cardiff City. Skuse has not played in multiple matches in either cup competition in a single season since.