Wilson began the 2012–13 season in fine form but on 27 October 2012 he suffered a broken fibula playing against Sunderland. Just before his injury Wilson had signed a new three-year contract. He returned to training in January 2013. He made his return from injury against Fulham on 23 February 2013. He ended the season with 20 appearances to his name as Stoke finished in 13th position and at the end of the campaign manager Tony Pulis was replaced with Mark Hughes, which was met with approval from Wilson.