Makoun made his first appearance return for the club, starting the whole game, in a 2–1 loss against Lorient on 16 September 2012. A month later on 20 October 2012, Makoun scored his first goal, since his return to the club, in a 2–1 win over champions Montpellier. After the match, he was named Man of the Match by the club's supporters. Since making his debut for Stade Rennais, Makoun became a first team regular for the side, playing in the midfield position. Having established himself in the first team, Manager Frédéric Antonetti praised Makoun's performance, with one goal in five starts and said to L'Equipe: ""He is an experienced player, positive and generous, It is such big help for a young team as ours."" In a 2–1 win over Paris Saint-Germain on 17 November 2012, Makoun received a red card after second bookable offence. After serving a one match suspension, he returned to the starting line–up, starting the whole game, in a 3–2 win against Troyes on 2 December 2012. However, his return was short–lived when Makoun suffered a thigh injury and was substituted at half time, as Stade Rennais drew 2–2 against Stade Brestois 29 on 8 December 2012. It wasn't until on 12 January 2013 when he returned to the starting line–up, in a 2–0 loss against Bordeaux. Makoun then contributed two assists for Mevlüt Erdinç, setting up a goal against SC Bastia on 20 January 2013 and then set up another goal against Lorient two weeks later on 2 February 2013. On 23 February 2013, Makoun scored his second goal for the club in a 2–2 draw against Sochaux. It was announced on 1 April that he would be joining Rennes on a permanent basis from 1 July. Makoun started the whole game in the Coupe de la Ligue Final, losing 1–0 against Saint-Étienne. At the end of the 2012–13 season, he went on to make thirty–two appearances and scoring two times in all competitions.