During the Second World War, Morgan-Giles served on during the Norwegian Campaign in 1940, escorting Atlantic convoys, and took part in the Battle of Oran. In 1941, he was sent to the Suez Canal, where he was in charge of the anti-magnetic mine campaign. In April of that year, he acted as a liaison with the Royal Air Force using Wellington bombers as torpedo bombers. During his time with No. 201 Group RAF at Dekheila he survived three serious aeroplane crashes (one of which he was the sole survivor). Following a period of staff training at the Royal Naval College, Greenwich, Morgan-Giles was then send to the Far East as Staff Officer Operations of Force W. There he accepted the Japanese surrender of Thailand.