Wells scored a penalty on the opening day of the 2012–13 season in an away match against Gillingham. He scored his second goal of the season on 25 August in a 5–1 win against AFC Wimbledon, and also assisted the fifth goal, crossing for James Hanson to score with a header. In September 2012, Wells suffered a hip injury. On 25 September, Wells came off the bench to score two late goals to help Bradford overturn a 2–0 deficit against Burton Albion in the League Cup third round, with Bradford going on to win the game 3–2 in extra time. At the end of September 2012, Wells signed a new three-year contract with the club, in a move praised by Phil Parkinson, the club's manager. In October 2012, Wells was banned by the club from celebrating his goals. As the January 2013 transfer window opened, Bradford City dismissed rumours linking Wells with a move away from the club. On 8 January 2013, he helped Bradford beat Premier League side Aston Villa 3–1 in the first leg of the semi-final of the League Cup by opening the scoring in the 19th minute. After appearing in the 2013 League Cup Final, Wells became the first player from Bermuda to appear in an English major cup final. Although Wells did not complete the game, prior to the match he spoke about being motivated by the recent death of a friend in a motorcycle accident, as well as how he was looking forward to facing opponents from a higher league. Wells hadn't scored for the club since 2 February 2013, until he scored the only goal of the game on 6 April 2013, in a 1–0 home victory against Northampton Town. Later that month, he was linked with a transfer to Burnley.