 After a spell as chaplain at Kashmir in 1865, he returned home to an appointment as rector of Stafford in 1867.Cowie was nominated Bishop of Auckland in 1869, and took up the position the following year, serving as such for more than 30 years.He was an important influence on the expansion and development of the Anglican Church in Aotearoa, New Zealand and Polynesia during the long period of his episcopate, and was also closely involved with the ordination of indigenous Melanesian clergy.