[2] Following the end of his career in 1990, Antonetti later began managing his former club, Corsican Division 1 side Bastia on youth level before taking charge of the senior team in 1994.

In his four years at the club, he guided them to the Coupe de la Ligue final in 1995, losing 2–0 against Paris Saint-Germain.

[citation needed] Antonetti took charge of Bastia as manager for the second time in June 1999, succeeding José Pasqualetti.

[citation needed] On 7 October 2001, Antonetti was revealed as the new manager of Saint-Étienne, penning a three-year deal.

He also spoke of his relationship with the club's president saying “With François Pinault, physically, we saw each other twice a year, once at the beginning of the season, another time in the middle, and then he came to the stadium with one or two matches".

[7] On 22 November 2015, Antonetti was appointed as the manager of Lille in place of Hervé Renard, signing a three-year contract.

On 22 November 2016, the club announced that they had parted company with Antonetti and that he had agreed to leave "in a friendly manner".

On 22 February 2022, Antonetti was involved in a fight following the full-time whistle with Lille's sporting director Sylvain Armand.