Jones made his comeback from the injury that ruled him out of the 2011 Rugby World Cup on 10 February 2012, playing 80 minutes for Shannon in their AIL game against Young Munster. He made his comeback for Munster in a Pro12 fixture against Treviso on 18 February 2012. Jones made his Heineken Cup debut in the quarter-final against Ulster on 8 April 2012. He missed Munster's league play-off semi-final against Ospreys on 11 May 2012 when he picked up a shoulder injury in training. The shoulder injury ruled him out for at least 4 months, as it required surgery.
