 After brief assignments in Huntsville, Alabama and Savannah, Georgia he was sent to Cuba in January 1899 to serve with the United States occupation force following the Spanish–American War.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.