In August 1900, Conner was reassigned to Washington Barracks (today named Fort McNair) in Washington, D.C. He was promoted to captain in 1901 and was transferred to Fort Hamilton, New York in November 1901 as commander of the 123rd Coast Artillery Company. He held this assignment until August 1905 when he began attendance at the Army Staff College at Fort Leavenworth, Kansas. He then served as adjutant of the Artillery sub-post at Fort Riley, Kansas from July 1906 to May 1907.