Duffy was awarded manager of the month in League Two for October 2013 after an unbeaten month with Clyde in the league and Scottish Cup, The team stretched that unbeaten run to ten games between October and December, but a 3–1 home defeat to Peterhead on 7 December ended that run. They secured a League Two play-off spot in the penultimate league match of the season with a 4–0 home defeat of Albion Rovers, but were beaten by East Fife after a penalty shootout in the semi-finals. Soon afterwards, Duffy resigned as manager of Clyde to take a similar position at Morton.