In 2009, his last season for Agritubel, Bouet also started off in the Grand Prix d'Ouverture La Marseillaise, this time claiming the 7th spot, just one minute and seven seconds behind winner Rémi Pauriol. That same month he finished 19th in the Tour du Haut Var and also won his first race of the season, the first stage of the Les 3 Jours de Vaucluse, including the leading jersey. In the end, he finished in the second spot behind teammate David Lelay. Bouet competed in his first Paris-Nice race afterwards, finishing in 64th position overall. At the Volta ao Alentejo Bouet won another stage race opener and wore the leader's jersey for two days until Héctor Guerra won the individual time trial in stage 3. However, with a third place in the 5th and last stage of the race he reclaimed the lead and took the overall win, one second ahead of Guerra. After finishing third in the general classification of the Rhône-Alpes Isère Tour Bouet focused on some of the classic races. He reached the finish of La Flèche Wallonne in 138th position, but did not finish Liège-Bastogne-Liège. Bouet was added to the Tour de France shortlist for Agritubel and was preparing for his first grand tour. With a win in the Boucles de l'Aulne and a seventh place in the Grand Prix of Aargau Canton he confirmed his form and made the final selection. In the third stage from Marseille to La Grande-Motte, a race won by Mark Cavendish, Bouet sprinted in the bunch to a ninth position, earning him his first and only top ten result of the Tour de France that year. A great result in the 20th stage from Montélimar to Mont Ventoux in which he finished in 17th place, Bouet ultimately secured a 69th overall ranking when finishing on the Champs-Élysées in Paris the day after. The 2009 season for Bouet ended in August after he became third in the second stage of the Tour de l'Ain where he claimed the 11th spot overall.