He joined Wolverhampton Wanderers on a three-month loan in September 2006. However, he returned to Middlesbrough on 15 November, after making just one first team appearance. He also had loan spells at Doncaster Rovers, scoring once against Gillingham and Darlington. During the 2007–08 pre-season, Jonathan Woodgate suffered an injury, that allowed Wheater to start in his place during pre-season. Wheater's form in pre-season, earned him a starting XI place for the opening day Premier League fixture – his form then continued, which triggered the transfer of Woodgate to Tottenham Hotspur, as Wheater became the first name on the 'Boro team sheet. Wheater was named in an understrength Middlesbrough side away to Bristol City in the FA Cup third round, when he saved his team with a goal as he burst forward from the back and scored the winner in a 2–1 at Ashton Gate Stadium. He signed a three-and-a-half-year contract extension in February 2008, which tied him to Middlesbrough until June 2011.