For his performance in 2012, Manaudou was awarded the Knight of the French National Order of the Légion d'Honneur in recognition of his "eminent merits" in swimming.

[3] In September 2021, Manaudou announced his engagement to his then-girlfriend, Danish swimmer and Olympic gold medalist Pernille Blume.

[4][5] The following month, Manaudou was present in the audience to support Blume as she competed in the dancing competition Vild med dans.

At the European Championships in Chartres, Manaudou won five gold medals including an individual title in the 50-meter freestyle with a time of 20.70.

[16] At the 2013 World Aquatics Championships in Barcelona, Manaudou won gold in the 4×100-meter freestyle relay with Yannick Agnel, Fabien Gilot, and Jérémy Stravius.

Manaudou won three gold medals at the 2015 World Aquatics Championships in Kazan, including the 50 m freestyle where he swam the fastest time ever in textile in 21.19.

Manaudou failed in his bid to qualify for the 2016 Olympic Games 100m freestyle when he only finished third at the French national championships held on 1 April in Montpellier.

He had been hoping to pull off a 50m-100m freestyle double at the 2016 Olympic Games in Rio de Janeiro but his time of 48.10sec was bettered by Jérémy Stravius (47.97) and Clement Mignon (48.01).

[21][22][23] Two days later, he achieved a time of 48.12 seconds in the preliminaries of the 100 metre freestyle to rank first before withdrawing from competing in the final.

[24] On day five, he won the gold medal and national title in the 50 metre freestyle with a 2023 World Aquatics Championships qualifying time of 21.62 seconds.

[25] Manaudou was the Opening Ceremony flag bearer for France along with the discus thrower Melina Robert at the Paris 2024 Olympic Games.