Foote was transferred to the Sixth Artillery, and he graduated from the Artillery School at Fort Monroe in 1888. He remained at the school as an instructor until 1891, and from 1892 to 1894, he served on the Intercontinental Railway Commission in Central America. He commanded cadets at the Vermont Military Academy from 1895 to 1897 and at the New York Military Academy from 1897 to 1898. Foote participated in the Spanish–American War, being in charge of U.S. Volunteer Engineers as well as serving as an aide during the Santiago Campaign. In the Philippines from 1899 to 1901, Foote commanded an artillery battery acting as infantry.