Sissoko started the 2009–10 campaign by displaying his attacking prowess as he scored six league goals in the club's first 12 matches. He opened the campaign scoring in the club's second league match of the season against Saint-Étienne in a 3–1 victory. On 20 September 2009, he scored in the club's 2–0 win against Le Mans and in the following week scored the opening goal in the club's 2–1 loss to Lyon. On 1 October 2009, Sissoko scored his first career European goal in a UEFA Europa League group stage match against Belgian club Brugge. The match ended in a 2–2 draw. On 24 October, Sissoko recorded his fourth league goal of the season in a 2–0 away victory over Lens. In the ensuing two weeks, Sissoko scored both openers in a 1–1 draw with Marseille and a 3–2 victory at home against Rennes. Sissoko's goalscoring slowed in the latter part of the season, scoring only one goal after the winter break against Valenciennes in a 3–1 win. He was a regular in the team for the rest of the season, but Toulouse failed to keep pace with the league leaders and finished a disappointing 14th.