Their biggest European triumph was reaching the UEFA Cup final in 1996. After qualifying for the Intertoto Cup, the Girondins won that competition to get a place in the UEFA Cup. They reached the final after victories over Vardar Skopje, Rotor Volgograd, Real Betis, a heroic quarter final win over AC Milan, and a semi-final win over Slavia Prague. In the UEFA Cup final, Bayern Munich prevented the Bordelais winning their first European Cup after a 5-1 defeat on aggregate.
Former Bordeaux midfielder Michel Pavon took charges of head coach in October 24, 2003. Because of health problems, he stood back and continued his career as scout on June 2005. Brazilian Ricardo became the new coach, until Laurent Blanc took over in 2007.