In 1940 he underwent training as on submarine warfare, and during the Greco-Italian War (1940–41) he served aboard submarines, undertaking patrols to intercept Italian shipping in the Adriatic Sea. On 31 December 1940 he was promoted to lieutenant. In March 1941 he received the War Cross for his service as an officer on board the submarine "Nirefs". In April 1941, as the German invasion of Greece had almost overrun the country, as much of the Greek fleet as could be saved was sent to the Allied-held Middle East. Although only a subaltern, Engolfopoulos took over command of "Nirefs" and led his vessel to the Middle East, where he joined the forces of the Greek government-in-exile. For this initiative he received his second War Cross on 14 September 1944. He then served as executive officer on board the destroyer "Pindos", with which he participated in the Battle of the Mediterranean as well as the Allied invasion of Sicily (July 1943) and the invasion of southern France ("Operation Dragoon", August 1944). He assumed himself command of the destroyer for a time in 1944. During the pro-Communist navy mutiny of April 1944, he participated in the boarding detachments that forcibly retook control of the ships and suppressed the mutiny.