 Cowie attended the Lambeth Conference in 1888 and 1897.He was elected Primate of the Anglican Church of New Zealand in 1895.In June 1902 it was announced that he would resign as bishop and primate, due to ill-health, but he died before stepping down the following week, on 21 June 1902 in Parnell, Auckland, and was buried at St Stephen's Cemetery.