After enlisting in 1939 Woodhouse was commissioned as an officer in the Royal Artillery in 1940, rising to the rank of colonel by 1943. He served most of his time during WW2 in Greece, and in 1941 he was one of the SOE officers sent to Crete to organise resistance forces behind enemy lines. In September 1942 he was parachuted to mainland Greece as Second in Command of the Harling Force headed by Eddie Myers. Following the success of this operation Myers and Woodhouse were ordered by SOE Cairo to stay on in mainland Greece, and form the British Military Mission (BMM).