David Wheater joined Owen Coyle's Bolton Wanderers in January 2011 to boost the Trotters' defensive options with Gary Cahill on the way out and only Zat Knight as the other option. Wheater struggled to break through at first but eventually found himself starting following Cahill's move to Chelsea. He made his debut in a FA Cup clash with Wigan at the end of January 2011.
During the second half of the 2011/12 season, David Wheater found himself as the first choice defensive option for Bolton and was partnered with either Knight or Tim Ream. He would suffer a cruciate ligament injury during the penultimate match of Bolton's last Premier League campaign. The knee injury would keep the big defender out of most of Bolton's 2012/13 Championship season. During the summer prior to the 2013/14 season, Wheater would sign a new three-year deal with the Whites, keeping him at the club until 2016.