On 3 August 2012, Lindegaard signed a new four-year contract with United, keeping him at the club until June 2016. He also took the number 13 jersey made vacant by the departure of Park Ji-sung, who had left the club for Queens Park Rangers.
Since the match against Norwich on 17 November 2012, first-choice goalkeeper David de Gea was sidelined with wisdom teeth problems. Lindegaard was kept in goal for United's next five games until De Gea was recalled for the Champions League match against CFR Cluj. Lindegaard returned to the first team on 1 December 2012, against Reading in a match which ended 4–3. After the match, he came in for criticism by former United goalkeeper Alex Stepney, who said that he lacks "authority at the back". After a long period on the bench as an understudy to De Gea, and with United having already secured the Premier League title a month earlier, Lindegaard started in goal for Sir Alex Ferguson's final game as United manager against West Brom at The Hawthorns; the match finished 5–5. That appearance was Lindegaard's tenth of the season, thus qualifying him to receive a Premier League winner's medal.
Lindegaard is one of the few footballers to have spoken out against the intolerance of homosexuality in football and the absence of openly gay players from the professional game. In a 2012 blog entry, he wrote,