At the start of the 2013–14 season, Makoun continued to be a first team regular for the side, playing in the midfield positions. He then played an important role against AC Ajaccio on 21 September 2013, setting up two goals for Foued Kadir to win 2–0. After missing one match, Makoun returned to the starting line–up, setting up the club's second goal of the game, in a 5–0 win against Toulouse on 26 October 2013. However, on 18 March 2014, French media reported claims that Makoun was involved in a bust up with Manager Philippe Montanier, which the player, himself, denied the claims. Amid to the incident, he scored his first goal of the season, in a 3–0 win against Bastia on 30 March 2014. This was followed up by setting up the club's first goal of the game, in a 2–2 draw against Bordeaux. A week later on 15 April 2014, Makoun scored the club's third goal of the game, in a 3–2 win against Angers SCO in the semi–finals of Coupe de France to send them to the final. However, he appeared in the starting line–up and played 68 minutes before being substituted in the Coupe de France Final against Guingamp, as Stade Rennais lost 2–0. During the match, Makoun suffered ankle injury that kept him out of the 2013–14 season. Despite this, he went on to make thirty–five appearances and scoring two times in all competitions.