At the start of the 2005–06 season, Makoun started the season well when he scored his first goal of the season, in a 3–3 draw against AC Ajaccio on 8 August 2005. Makoun continued to regain his first team place, playing in the midfield position. His second goal for the side came on 17 September 2005, in a 4–0 win against OGC Nice. A month later on 22 October 2005, he scored his third goal of the season, in a 2–0 win against FC Nantes. His performance against Manchester United in the UEFA Champions League earned him praises from the British media. After spending January with his international duty, Makoun returned to the first team, starting the whole game, in a 0–0 draw against Paris Saint-Germain on 12 February 2006. However, he was then sent–off for a straight red card in the 50th minutes, in a 1–0 win against AS Monaco on 26 February 2006. After serving a one match, Makoun returned to the starting line–up on 9 March 2006, helping the side win 1–0 against Sevilla in the first leg of the UEFA Cup. Two weeks later on 25 March 2006, he made his 100th appearance for the side, in a 2–2 draw against Strasbourg. It wasn't until on 6 May 2006 when Makoun scored his fourth goal of the season, in a 4–0 win against Lyon. As a result, the win saw the club qualify for the UEFA Champions League next season. At the end of the 2005–06 season, he went on to make forty–three appearances and scoring four times in all competitions.