In 1805, Merlin's regiment was recalled to the Grande Armée and he served in it for the next three years, fighting at the battles of Austerlitz, Jena and Friedland. He distinguished himself at the capture of Lübeck, and promoted to Major on 20 February 1807. On 20 July 1808 he became a "chevalier de l'Empire", and served the following year under Marshal Bernadotte in Antwerp.