Mullan also made 3 appearances and scored 1 goal during the group stage of the 2011–12 CONCACAF Champions League. Mullan signed a multi-year contract extension with Colorado on December 5, 2011. Mullan recorded his first assist of the 2012 season on April 1, helping Colorado get a 2–0 win against the Chicago Fire. On April 14, 2012 the Rapids lost 1–0 at the Seattle Sounders. It was Mullan's first game in Seattle since he had injured Steve Zakuani in 2011 and Sounders fans booed him every time he touched the ball. On May 6, Mullan had 2 assists as the Rapids beat FC Dallas 2–0. He scored his first goal of the season on June 20 in a 2–1 loss to the Earthquakes. On July 7, Mullan and the Rapids visited the Sounders, losing 2–1. During the game, Zakuani made his return from injury, coming on as a late substitute. After the match Mullan and Zakuani swapped jerseys and hugged each other. Zakuani said after the game "I forgave him a long time ago, but I think it is good for the public to see, for closure." On August 4, Mullan played in his 300th MLS regular season game as the Rapids beat Real Salt Lake 1–0. He underwent knee surgery on October 18, causing him to miss the final 2 games of the regular season. Mullan ended the season with 2 goals and 7 assists from 28 regular appearances. He had been dealing with pain in his knee throughout the season and with the Rapids already eliminated from the playoffs, Colorado and Mullan went ahead with the surgery. It was the first time Mullan had missed out on the playoffs during his MLS career. At the start of the 2013 season, Rapids coach Óscar Pareja converted Mullan to a left-back. He played there for the first 4 games of the season before being switched to a right-back. Mullan did not appear during the final three months of the season, partly due to injuries, but also because Pareja preferred different players in that position. Mullan made 16 appearances and had 2 assists during the regular season, helping the Rapids qualify for the playoffs. However he would not appear during their one playoff game. On December 10, the Rapids declined Mullan's contract option for the 2014 season. On January 14, 2014, Mullan signed a new contract with the Rapids. He had