Skuse returned to his more familiar midfield position ahead of the 2012–13 season. On 6 November, he picked up an injury away to Birmingham, and missed the next month and a half. The club were in the relegation zone, in the middle of a seven match losing streak. He missed the whole month of February with a separate injury picked up against Watford. At the end of his last season with the club, Bristol City could not avoid relegation to League One, and Skuse left the club on a free transfer, although he later said the two were not related. His final appearance for the club came on 1 April 2013, in a draw against Sheffield Wednesday, and Skuse made 25 appearances in the league in his last season. He represented Bristol City 307 times across all competitions during his tenure, scoring 9 goals.