After serving in Montana, North Dakota, and Nebraska, Ely became a Professor of Military Science and Tactics at the University of Iowa, serving in this position from 1897 to 1898. During the Spanish–American War, Ely reported to his regiment at Camp Wikoff and then served in the Philippines from 1899 to 1901. In addition to commanding General Frederick Funston's mounted scouts, Ely served as a regimental and district adjutant in Luzon. He received his first Silver Star due to his efforts in the Philippines. He attended the German Army Maneuvers in 1906, and he again served in the Philippines from 1907 to 1912. Ely served with Funston on the United States occupation of Veracruz in 1914.