Pat Lam left Connacht for Bristol in summer 2017, and was replaced by Kieran Keane, who kept Muldoon on in his role as captain. In January 2018, Muldoon announced that he would be retiring at the end of the season. His final game came against Leinster in the Pro14 on 28 April 2018 at the Sportsgrounds. The result was a 47–10 win for Connacht, with Muldoon scoring his last ever points for the province by converting the team's final try of the day.