On 20 January 2011, Wheater completed a move to Bolton Wanderers on a three-and-a-half-year contract following a few weeks of negotiations for an undisclosed fee, and made his debut on 29 January in the FA Cup game at home to Wigan Athletic. He made his league debut when coming on as a first-half substitute for the injured Zat Knight in the 2–0 home win over Everton on 13 February. On 24 September, in his first league start of the 2011–12 season replacing the ill Gary Cahill, Wheater received a red card for holding back Theo Walcott during Bolton's game at Arsenal. Two months later on 26 November, while playing in the right-back position, he received his second dismissal of the season when challenging Everton winger Diniyar Bilyaletdinov in a challenge which was deemed a red card by the referee Michael Oliver, which resulted in a four-game ban.