During World War I, Malone commanded Royal Naval Air Service (RNAS) planes in the Cuxhaven Raid on 25 December 1914. From August 1914 to March 1915, he captained , a cross-channel steamer converted to a seaplane carrier. From March 1915 to April 1916, he captained , another steamer converted to a seaplane carrier. Under Malone's command, seaplanes from "Ben-my-Chree" were the first on record to carry torpedoes and they torpedoed three enemy vessels in 1916. Malone then took over command of the East Indies and Egypt Seaplane Squadron, for which he was awarded the Fourth Class of the Order of the Nile.