On 7 May 2012, he was ruled out of action for up to nine months after rupturing an anterior cruciate ligament in his right knee in Bolton's 2–2 draw with West Bromwich Albion the previous day. His return to the first team came ten months later as he came on as a late substitute in Bolton's 4–1 win against Hull City. Wheater signed a contract extension on 21 July 2013, extending his contract until summer 2016. At the end of the 2015–16 season, the club confirmed that he would be leaving when the contract expired. Despite this, Wheater still trained with the club and played in most of their pre season friendlies for the 2016–17 season, as a trialist player. He then re-signed for the club on a one-year contract on severely reduced wages.