Flamini saw limited playing time towards the end of 2009–10 season due to the great form of club captain Massimo Ambrosini. In the following season, Flamini became an important asset of the team that would win its 18th "scudetto", playing many games as starter and scoring two goals against Bari and Bologna, respectively. After playing as a rotation role in the 2010–11 season, he injured himself in a pre-season training session, suffering a serious knee injury which required an operation. Flamini spent the entire 2011–12 season out.