He made his Serie A debut on 30 August 2008 in a 2–1 loss to Bologna. Initially, Flamini did not enjoy the number of starts or appearances for the Italian team, and was regarded as a utility player at Milan. Nevertheless, injuries to other players and his consistent good form helped him to cement a starting place at San Siro. With Milan failing to find a stable defence and a lack of a fit, consistent and reliable right back, Gianluca Zambrotta was switched to the left flank to help Flamini develop as a tenacious right back. After stating that his preferred position is in the midfield, Milan re-deployed him as a defensive midfielder.