On 5 October 1803, Barrois received promotion to colonel commanding the 96th Line Infantry Regiment. His unit was stationed at Mont Cenis in the Alps under the orders of Michel Ney and he became a Chevalier of the Legion of Honor. The 96th Line was assigned to the brigade of Jean Gabriel Marchand in the division of Pierre Dupont de l'Étang. Barrois sat on the military commission that condemned Louis Antoine, Duke of Enghien to death. When the War of the Third Coalition broke out, he won distinction at the Battle of Haslach-Jungingen on 11 October 1805. In this action, Dupont's 5,350 infantry, 2,169 cavalry and 18 guns fought 25,000 Austrians to a standstill. Dupont's division also fought at the Battle of Dürrenstein on 11 November. After this campaign, Barrois was made a Commander of the Legion of Honor.