In the 2012–13 season, Muldoon did not play as regularly as the previous season, again due to injury. He featured in only two of Connacht's games in the 2012–13 Heineken Cup, but managed to score his first Heineken Cup try against Zebre on 13 October 2012. In the 2012–13 Pro12, Muldoon played 16 games, starting in nine of them.