At the start of the 2003–04 season, Makoun scored his first goal for the club, as they beat the defending champion, Lyon, to win 1–0. He quickly became a first team regular for the side under the management of Puel, who was impressed with his quality performance. As the season progressed, Makoun began to develop for the side by displaying "good technique and a lucidity which regularly allows him to play his role as a passer." It wasn't until on 31 October 2003 when Makoun scored his first goal of the season, in a 2–0 win against Nîmes Olympique in the second round of the Coupe de la Ligue. Two months later on 17 December 2003, he scored his second goal of the season, in a 3–2 loss against Saint-Étienne in the last 16 of the Coupe de la Ligue. At the end of the 2003–04 season, Makoun went on to make thirty–four appearances and scoring three times in all competitions.