At the start of the Napoleonic Wars, Marcognet was a general officer commanding a brigade in Marshal of France Michel Ney's corps. He led his troops at Günzburg, Elchingen, and Scharnitz in 1805. In the 1806-1807 campaign, he led his brigade at Jena, Magdeburg, Eylau, Guttstadt-Deppen, and Friedland. After Ney's corps transferred to Spain, he fought at Tamames, Alba de Tormes, Ciudad Rodrigo, Almeida, Bussaco, Torres Vedras, Casal Novo, and Fuentes de Onoro.