He received promotion to Major in the 5th Artillery Regiment on September 14, 1883. From September 1884 to November 1886, Miller was assigned to Fort Hamilton, New York, including a leave of absence for illness from June to October 1885. From November 1886 to June 1888, Miller was inspector of rifle practice and acting ordnance officer for the Military Division of the Atlantic. He was commander of the post at Fort Columbus, New York from July to December 1888. From January 1889 to October 1894, Miller was again assigned to the staff of the Artillery School, this time as superintendent of instruction for Field Engineering, Electricity, Mechanical Engineering, and the Art of War. On February 27, 1890, Miller was promoted to brevet colonel for gallant and meritorious service on April 17, 1873 at Lava Beds, California during the Modoc War and Clearwater, Idaho on July 11 and 12, 1877 during the Nez Perce War. He was promoted to lieutenant colonel in the 1st Artillery Regiment on October 10, 1894. Spanish–American War Miller commanded the 1st Artillery Regiment and Fort Hamilton, New York from October 1894 to October 1896. He remained in command when the regiment moved to St. Francis Barracks in Saint Augustine, Florida and also commanded the post. Miller was promoted to colonel on April 30, 1897, and took command of the 3rd Field Artillery Regiment and the post at Fort McDowell, California. At the start of the Spanish–American War in April 1898, Miller assumed command of all the Coast Artillery forts protecting San Francisco Bay. In addition, he served on wartime boards that considered the retirement and promotion of officers. In May 1898, Miller was promoted to brigadier general of United States Volunteers. From May to July 1898, Miller commanded 1st Brigade, Eighth Army Corps. From July to November 1898, Miller commanded the Eighth Army Corps' Independent Division and the garrison troops at The Presidio of San Francisco. Philippine–American War From November to December 1898, Miller commanded the Independent Division of the Eighth Army Corps while en route to the Philippines. Upon arrival, he took part in the Philippine–American War as commander of the 1st Separate Brigade of the Eighth Army Corps. The brigade was immediately ordered to take control of the city of Iloilo on the island of Panay from Spanish troops who were departing after the end of the Spanish–American War. Filipino insurgents occupied Iloilo after