In the 2007–08 season Duff picked up a serious injury during the Championship match against Crystal Palace at Turf Moor. The injury ruled Duff out for almost a year, causing him to miss the first half of the following campaign. He suffered multiple ligament damage and hamstring damage as well as a cruciate knee injury. Duff started his first Premier League match on Boxing Day 2009 against Bolton Wanderers at Turf Moor, having made his debut as a substitute in the preceding game versus Wolverhampton Wanderers. In doing so, he completed the rare feat of having played in each of the top eight tiers of English football in ascending order during his career: the Hellenic League with Carterton Town, the Southern League (Midland Division) with Cirencester Town, the Southern League (Premier Division), Conference (prior to its 2004 re-organisation), League Two and League One with Cheltenham Town, and the Championship and Premier League with Burnley.