1995 saw Protat move up to the 500cc class riding an ROC Yamaha. In 1996, he was the highest ranking privateer in the 500cc class, finishing the season in 15th place. Protat's final season in the 500cc class was in 1997 riding a Honda.
He scored 12 points in the 250cc Grand Prix class and 41 points in 500cc category. In 1998 and 1999 he participated in the World Superbike Championship for Ducati. In 1999 he was vice champion of France on a Ducati superbike. In 2000 and 2001 he won the French Superbike Championship on a Ducati Superbike. In 2002 he was vice champion of France on Ducati. In 2006, he won the 24 Hours of Le Mans motorcycle endurance race along with Olivier Four and Daniel Ribalta-Bosch riding a Honda CBR.