 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.