He was first in Athens, and then in German-occupied Crete collecting intelligence and helping British solders escape from the island where he learned 'to feed on snails, mountain grass and ground acorns'. After a spell at a training school in England he was parachuted as second-in-command with a small British team into mainland Greece with the object of making contact with local resistance fighters and sabotaging the main railway line. This was successfully achieved when the railway viaduct at Gorgopotamos was blown up, one of the most spectacular wartimes acts of resistance in occupied Europe, and an act that gave great momentum to resistance to the Germans. Woodhouse stayed in the mountains for the rest of the occupation, becoming head of the now Allied Military Mission. In his unpublished 1945 report on the Mission, he wrote:
"Nothing matters so much in this story as the Greek mountains. The rolling downs of Olympus, the precipitous ravines of Agrapha, the orchards of Pelion, the staggering crags of Smolikas, the long, thin ridge of Taygetos, the pine forests of Giona, are almost individual characters in the story, their roles perpetually changed by sun and snow and rain. Without them no guerilla movement could have been born."