In November 1881, Miller returned to coast artillery defense of San Francisco Bay, this time at
Point San Jose. From November 1881 to June 1885, Miller was assigned to coast artillery duty at
Fort Preble, Maine. From July to December 1885, he was assigned as professor of military science at the
University of Vermont. He was then assigned as adjutant of the Artillery School, where he remained until March 1887. Miller was next assigned as quartermaster of the 4th Artillery Regiment at
Fort Adams, Rhode Island. In November 1887, Miller was promoted to
captain. Miller was assigned to duty at
Fort Totten, New York from December 1887 to July 1888. In August 1888, Miller was assigned to oversee construction of the buildings at
Fort Sheridan, Illinois, where he served until January 1890. He was then appointed to head the Constructing Bureau in the office of the
Quartermaster General of the United States Army, where he served until January 1898. Miller was assigned as Fort Monroe's quartermaster in January 1898, and in February he received promotion to
major. With the outbreak of the
Spanish–American War in April 1898, the army rapidly expanded, and Miller was assigned to the staff of the army's quartermaster general. In May, Miller was promoted to
lieutenant colonel of
United States Volunteers and assigned as chief quartermaster of volunteers. In July 1898, Miller resigned his commission in the volunteers and was appointed to command the quartermaster general's Bureau of Regular Supplies and Wagon Transportation with the temporary rank of
colonel. In March 1899, Miller resigned from the United States Volunteers and returned to his permanent rank of major. ==Later career==