Makoun started well on his debut for Olympique Lyonnais when he scored the club's first goal of the season, in a 3–0 win over Toulouse. Two weeks later on 23 August 2008, Makoun scored his second goal of the game, in a 2–0 win against Grenoble Foot. Since making his debut for Olympique Lyonnais, he quickly established himself in the starting eleven for the side, playing in the midfield position. In a UEFA Champions League match against Steaua Bucharest, Makoun set up the club's first goal of the game when they were 2–1, as they made a comeback with a 5–2 win. A month later on 25 November 2008, he scored his first UEFA Champions League goal, in a 2–1 win against Fiorentina. He then scored two goals in two matches between 8 February 2009 and 15 February 2009 against Nice and Le Havre (which he also made a double assist during the match). Makoun scored two more goals in March, scoring against his former club, Lille in the round of 16 of Coupe de France, which Lyon lost 3–2 and Barcelona in the last-sixteen second leg of the UEFA Champions League, which Lyon lost 5–2. Two months later on 12 May 2009, he scored twice for the side, as they won 3–0 against FC Nantes. At the end of the 2008–09 season, Makoun made forty–six appearances and scoring ten times in all competitions.