For the 2007–08 season, newly appointed Lyon manager Alain Perrin appointed Cris as the new captain . On 11 August 2007, Cris was injured in a game between Lyon and Toulouse, tearing ligaments in his right knee during a collision with Johan Elmander. Cris made his return to the squad on 1 March 2008 in a 1–0 win over Lille. The match was held at the Stade de France. On 17 March 2012, Cris suffered a calf injury in a 1–0 derby win over Saint-Étienne that ruled him out for a month.