On 1 June 2017, Wheater signed a new one-year deal with the club with a contract extension option. Wheater's only goal of the 2017–2018 season came on the final day, scoring the second goal in a 3–2 win against Nottingham Forest, which kept Bolton in the Championship at the expense of Barnsley and Burton Albion. Bolton took up the contract extension option on 7 June 2018, extending his contract for another year For the 2018–2019 season, Wheater was captain. Wheater was released at the end of his contract in June 2019, however despite this he took part in most of Bolton's pre-season matches for the 2019–2020 season, turning down contract offers from Kilmarnock, Salford City, and Oldham Athletic as he wanted to stay at Bolton. Wheater had agreed a one-year contract, on severely reduced wages, to re-sign for Bolton, with a second year if he played in 30 matches, though Oldham owner Abdallah Lemsagam talked him out of it, stating that the lower wages wouldn't be fair to his family.