As the club manager of Bordeaux, Baup won the French Division 1 championships in 1999 and the Coupe de la Ligue in 2002.

[2][3][4][5] On 2 August 2012, Baup oversaw his first competitive match as Marseille manager, a 1–1 away draw in the 2012–13 Europa League third qualifying round first leg against Turkish club Eskişehirspor.

[6] Seven days later, Marseille beat Eskişehirspor 3–0 in the return leg, winning the tie 4–1 on aggregate and thus secured a place in the 2012–13 Europa League play-off round.

In the afternoon of 7 December 2013, the club announced on its website that Baup was no longer the Olympique de Marseille manager.

The club president (Vincent Labrune) and Baup had earlier held a meeting right after the end of the training session conducted in the morning of 7 December 2013.

"The board feel that, after 17 league matches into the season, results have not corresponded with our objectives and a firm decision had to be taken to get the team moving in the right direction again in the coming weeks," read a statement on the club's official website.