Ahead of the 2006–07 season, Makoun was linked a move away from Lille over the summer, but he made it clear of staying at the club. Makoun continued to regain his first team place, playing in the midfield position. He then helped the side qualify for the UEFA Champions League Group after beating FK Rabotnički 4–0 on aggregate in both legs. It was announced on 10 October 2006 that Makoun signed a contract extension with the club, keeping him until 2011. Four days later on 14 October 2006, he set up the club's equalising goal, in a 1–1 draw against Troyes. Three days later on 17 October 2006, Makoun scored his first goal of the game, in a 3–1 win against AEK Athens. Three months later on 24 January 2007, he scored his second goal of the game, in a 1–0 win against Paris Saint-Germain. Despite being sidelined on four occasions during the 2006–07 season, Makoun made forty–five appearances and scoring two times in all competitions.