Following the signings of Erik Pieters and Marc Muniesa, assistant manager Mark Bowen stated that Wilson could revert to a midfield position in 2013–14. As expected Wilson began the season in a centre midfield spot and he stated that he is enjoying the change in style under Hughes. He failed to hold down a regular place in midfield and after spending a few months on the bench he returned to the starting line-up in December 2013, playing at centre-back after injury to Robert Huth. Wilson continued to play alongside Ryan Shawcross in centre of defence until the end of the 2013–14 season as Stoke finished in 9th position. Wilson played 30 times for Stoke in 2014–15 as Stoke again finished in 9th position.