At the start of the 2009–10 season, Makoun continued to regain his first team place, playing in the midfield position. He then scored his first goal of the season, in a 3–0 win against AJ Auxerre on 22 August 2009. This was followed up by setting up the club's third goal of the game, in a 3–1 win against AS Nancy. Makoun then helped the side qualify for the UEFA Champions League Group after beating Anderlecht 8–2 on aggregate. However, he was often inconsistent in midfield, which was subjected to criticism from Lyon fans and demands Makoun to leave the club, despite having played regularly. Nevertheless, Makoun set up a goal for Lisandro López, in a 5–5 draw against rivals, Marseille on 8 November 2009. Makoun then helped the club qualify for the knockout stage with thirteen points in the Group Stage, finishing in second place. However, he received a red card after a second bookable offence in a 0–0 draw against Toulouse on 7 February 2010. Amid to suspension, Makoun scored the only goal in Lyon's first leg UEFA Champions League knockout round win over Real Madrid at Stade Gerland by hitting a looping shot from 25 yards out over the head of goalkeeper Iker Casillas and into the top corner of the net in the 47th minute. After the match, Makoun said his goal 'delighted' him. Eventually, Lyon went through to the next stage in the Champions League after a 1–1 draw in a second leg. However, Lyon was eliminated in the semi–finals in the UEFA Champions League after losing 4–0 against Bayern Munich on aggregate. Despite being sidelined on three occasions later in the 2009–10 season, he made forty–one appearances and scoring two times in all competitions.