In July 2003, Sissoko made the trek down south to the Haute-Garonne department to sign with professional club Toulouse FC. He signed an "aspirant" (youth) contract and was placed in the club's under-14 team. Sissoko spent three years developing in the club's youth academy alongside future teammates Cheikh M'Bengue and Étienne Capoue before earning a call up to the club's reserve team in the Championnat de France amateur, the fourth level of French football, ahead of the 2006–07 season. Sissoko appeared in 18 matches during the amateur season, quickly becoming one of the club's most sought after prospects. Prior to signing his professional contract with Toulouse, he garnered interest from English clubs Liverpool and Bolton Wanderers.