From 1951 to 1953, Choo coached the Indonesia national team on an honorary basis. The team toured Hong Kong in 1953, achieving wins over professional Hong Kong outfits. Choo was appointed Malaya national coach in 1958. He led the team to three Merdeka Tournament titles from 1958 to 1960. With Choo, Malaya also won the 1961 Southeast Asian Peninsular Games football competition and the bronze at the 1962 Asian Games. Choo left Malaysia and returned to Singapore in 1964. He was appointed Singapore national coach over four stints from 1964 to 1977. He won the Malaysia Cup in 1977, twelve years after Singapore's last triumph. His achievements earned him the 1977 Coach of the Year award. The following year, he was honoured with the Pingat Bakti Masyarakat medal for his services to Singapore football.