In the 2012–13 season, Abdou continued to establish himself in the first team, playing in the midfield position for the side and formed a partnership with Josh Wright. During a match against Bolton Wanderers on 6 October 2012, Abdou suffered ankle injury and played through the game, as Millwall won 2–1. He soon recovered after a two weeks international break and started the whole game, in a 2–2 draw against rivals, Crystal Palace on 20 October 2012. Following this, Abdou signed a two–year contract with the club, keeping him until 2015. After missing two matches in mid–December, due to suspension and given a compassionate leave, Abdou then appointed as a captain in a FA Cup match, in a 1–0 win over Preston North End. After the match, he said that given the captaincy was an honour for him. He again captained the side once again on 16 February 2013 against Luton Town in the fifth round of the FA Cup and beat them 3–0 to progress to the next round. Three days later on 19 February 2013, Abdou captained the side for the third time this season, in a 5–1 loss against Peterborough United on 16 February 2013. AManager Jackett mentioned Abdou in the post-game interview, quoting: "You could see the danger from the sidelines – not enough players on the pitch could sense that danger and were able to react or cut the ball out – probably Jimmy Abdou apart." After appearing two matches as an unused substitute bench in early–April, Abdou scored on his return to the starting lineup, in a 2–1 loss against Sheffield Wednesday on 9 April 2013. At the end of the 2012–13 season, making 39 appearances and scoring once, Kenny Jackett, a manager who signed him, left the club.