At the start of the War of the Fourth Coalition, Marcognet commanded a brigade in Gaspard Amédée Gardanne's division of Marshal Michel Ney's VI Corps. The brigade consisted of the 1st and 2nd Battalions of the 25th Light Infantry Regiment. He led his troops at the Battle of Jena on 14 June 1806 and at the Siege of Magdeburg from 22 October to 11 November. Ney's corps arrived at the Battle of Eylau at 7:15 PM on 8 February 1807.