 Duffy failed to play in any of Connacht's 2012–13 Heineken Cup matches, while his appearances in the 2012–13 Pro 12 went down to 16, 3 of these coming from the bench.For the 2013–14 Pro 12 and Heineken Cup, Duffy started out the season sharing the captaincy with both Muldoon and Connacht's longest serving player, Michael Swift.However, after a poor run of form culminating in a 43-10 defeat against Edinburgh, Craig Clarke, a New Zealand native and the former captain of the Chiefs, was made Connacht's team captain with Duffy and the others continuing to "lead off the field".