On 24 February 2012, Munster announced that Howlett had extended his contract until the end of the 2012–13 season. On 24 August 2012, it was announced that Howlett would take over from Paul O'Connell as the Munster squad captain for the 2012–13 season. He underwent successful knee surgery in late January 2013, and returned to action after the surgery on 2 March 2013. On 14 May 2013, it was confirmed that Howlett, after receiving medical advice, would retire from rugby due to a shoulder injury he sustained playing against Glasgow Warriors in March 2013.