His debut came on 28 August 2012 in a 2–1 defeat against Crawley Town in the League Cup second round. However, Lonergan found himself competing with Ádám Bogdán over the first choice goalkeeper spot. On 19 October 2012, Lonergan suffered a knee injury, which he sustained in training and was sidelined for two months. Lonergan's first experience in front of the Reebok Stadium crowd was the 2–2 draw between Wanderers and Sunderland in which he was named Man of the Match for Wanderers following appreciation of his contribution following saves from Steven Fletcher on 5 January 2013 and played against them in the FA Cup third round replay on 15 January 2013, where he kept a clean sheet, in a 2–0 win to send them through to the next round. Lonergan's first league game for Bolton came on 5 March 2013, as Bolton beat local rivals Blackburn Rovers by a single goal. Lonergan made four more appearance and kept two more clean sheets before Bogdán returned from injury and went on to make eleven appearance in all competitions.