He returned to Malaya as a squadron commander in 1955. He was appointed a Member of the Order of the British Empire in 1957 for his services in command of D Squadron 22nd SAS Regiment in Malaya. In 1958, he transferred from the Dorset Regiment to the Parachute Regiment and commanded a company in the 3rd battalion before being appointed second-in-command of 22 SAS in 1960. In 1962, he was chosen to command the regiment. Following the Brunei Revolt, it went to Malaysia in 1963 to address the Indonesian threat. Recalling the approach in Malaya, SAS teams organised jungle tribes to gather intelligence. In January 1964, Woodhouse launched one of his squadrons on Operation Claret with a mission to locate camps from which Indonesian incursions were launched, and to identify their routes into Sarawak. He convinced his SAS troopers that intelligence was of more long-term value than to inflict limited casualties. When Commonwealth forces brought the Indonesian incursions to an end in 1965, 22 SAS was withdrawn.