At the start of the 2011–12 season, Duffy's Clyde defeated his ex managing team Brechin City 4–2 away and East Stirlingshire 7–1. On 1 February 2012, Duffy was appointed on to the club's board. His Clyde team could only muster back-to-back two ninth-place finishes in seasons 2011–12 and 2012–13.Montrose 5–0 Clyde Clyde FC. 06-05-2012. Retrieved 08-05-2015.Clyde 1-2 Stirling Albion Clyde FC. 04-05-2014. Retrieved 08-05-2015. Nairn County of the Highland League knocked his Clyde team out of the Scottish Cup after a replay in October 2012.Nairn County 3-2 Clyde Clyde FC. 06-10-2012. Retrieved 08-05-2015.
