 Jones started the 2011 – 12 season well scoring against Norwich City and twice against FC Thun in the UEFA Europa League. With Stoke signing Peter Crouch at the end of August, Jones found himself out of favour and was restricted to cup and European matches. This has led to speculation that Jones could be leaving the club in the 2012 January transfer window but Pulis insists that he is still in his plans. He scored an historic goal for Stoke against Dynamo Kyiv to earn them a 1 – 1 draw which secured Stoke's qualification to the knock-out stage of the Europa League. In 2012 – 13 Jones remained behind Crouch in Pulis' starting line-up restricting him to cameo appearances off the bench. He regained his place in December 2012 after injury to Crouch and scored his first Premier League goal for sixteen months in a 1 – 1 draw with Everton. Jones continued his revival scoring against Liverpool on boxing day, and against his old club Southampton on 29 December. Jones lost his place once Crouch had returned to the side and he ended the season on a sour note as he was involved in a dressing room bust-up with Glenn Whelan. At the end of the season Tony Pulis was replaced by Mark Hughes and Jones was critical of the style of football played under Pulis.
