Following the departure of Emana to Spain, Casanova put Sissoko into the box-to-box midfielder role ahead of the 2008–09 season to accommodate emerging defensive midfielder Étienne Capoue into the starting lineup, as well as Étienne Didot, who arrived from Rennes. The move allowed Sissoko to retain his defensive duties, but also showcase his attacking skills. He began the season featuring primarily as a substitute under Casanova, but by December, Sissoko had become a regular in the starting eleven. On 24 January 2009, he scored his first goal of the season against amateur Alsatian club FCE Schirrhein in an 8–0 thrashing in the Coupe de France. It was a memorable goal with Sissoko running nearly the entire pitch with the ball at his feet, eluding several Schirrhein players, before finishing at the six-yard box. Toulouse reached the semi-finals of the competition before losing 2–1 to the eventual winners Guingamp. In the league, Sissoko was a key contributor in helping a refurbished Toulouse side finish 4th in the league, leading to qualification for the newly created UEFA Europa League. He scored his first goal of the league campaign on 7 February in a 2–0 victory over Le Mans. Sissoko also scored goals in victories over Derby de la Garonne rivals Bordeaux and Paris Saint-Germain. In total, he made 40 appearances and scored five goals. For his efforts, he was nominated for the UNFP Young Player of the Year, along with teammate Capoue who also had an outstanding season.