Lonergan was revealed as Leeds' new captain on 20 January, replacing the departing captain Jonny Howson, with Patrick Kisnorbo out until the end of the season. Lonergan was replaced as Captain by Robert Snodgrass, who was appointed the new Leeds United captain by new Leeds manager Neil Warnock in his first game in charge against Portsmouth on 25 February. After a string of clean sheets, Lonergan conceded seven goals in a 3–7 loss against Nottingham Forest. Lonergan saved a penalty against Millwall's Darius Henderson in the following game to earn Leeds a crucial 1–0 victory.