Marcognet became a member of the Légion d'Honneur on 10 December 1804 and received the cross of the Légion d'Honneur from Emperor Napoleon on 14 June 1805. In the War of the Third Coalition he was assigned to Jean-Pierre Firmin Malher's 3rd Division of Marshal Michel Ney's VI Corps. At the Battle of Günzburg on 9 October 1805 he led Malher's center column in an attempt to seize the Danube bridge. His troops overran the Austrian covering force, capturing Konstantin Ghilian Karl d'Aspré, 200 men, and two cannons. Marcognet ordered four cannons to provide covering fire as the French tried to rebuild the destroyed span, but the troops were driven back by intense hostile fire. Mahler's division was present at the Battle of Elchingen on 14 October but it was mostly kept in reserve. Marcognet fought at Scharnitz in the Tyrol on 4 November.