On 1 June 2008, Jones suffered a knee ligament injury in a collision with goalkeeper David James in the seventh minute of Trinidad & Tobago's 3–0 defeat against England. He made his first appearance of the 2008–09 season playing for 60 minutes in Sunderland reserve team's 2–0 victory against Wigan Athletic., followed by a return to Sunderland's first team in the Tyne–Wear derby on 25 October 2008 as a second-half substitute, when he helped Sunderland to secure a 2–1 victory over their local rivals. His first goal following his return came on 12 November in a 2–1 League Cup defeat against Blackburn Rovers. He continued his recovery from injury with a goal, again against Blackburn, on 15 November 2008 as Sunderland won 2–1.
