Duffy rejoined Connacht in late 2006, going on to become a mainstay of the Connacht team. He was named as captain for the 2011–12 season, replacing his Galwegians clubmate and fellow Ireland cap-holder John Muldoon in the role. In the 2011–12 Heineken Cup Duffy scored a try against former club Harlequins, as well as against Gloucester. He scored 4 tries for Connacht in the Pro 12, starting all 22 of their games, as well as all six of their Heineken Cup matches.