Winder was commissioned as a colonel in the U.S. Army at the start of the War of 1812. He participated in the battle of Frenchman's Creek in 1812. Promoted to brigadier general, he took command of the 3rd Brigade in Henry Dearborn's Army of the North and led his brigade in the amphibious landing on the Niagara Peninsula during the Battle of Fort George. He was one of two acting commanders of the American army at the Battle of Stoney Creek in July 1813, where he was captured, along with fellow commander, John Chandler.