In 1938, Cowley was called to serve as president of the church's New Zealand Mission. He directed the affairs of the missionaries in New Zealand and oversaw church proceedings in the area. The mission included around 60 missionaries and 9,000 church members at the time, and Cowley was able to visit with many of the people he had met on his first mission. As World War II began, the church called the missionaries serving overseas back home to the United States, but Cowley and his family remained in New Zealand throughout the war. He was affectionately called "tumuaki," meaning president, by the Māori members of the church. During his service, he adopted a Māori baby boy, Duncan Nopera Meha Cowley (Toni). Cowley was known by both members and non-members alike for his dedication to the Māori people. He returned home in 1945.