Emmanuel Kiwanuka Nsubuga studied at the seminary of Katigondo the subjects philosophy and Catholic theology. He received the sacrament of Holy Orders in 1946 and then worked as a parish pastor. From 1961 to 1966 he served as Vicar General of the Archdiocese of managing Kampala.
1966 Pope Paul VI appointed him. Archbishop of Kampala. He received his episcopal consecration on October 30, 1966 Cardinal Laurean Cardinal Rugambwa, Archbishop of Dar es Salaam in Tanzania; Co-consecrators were later Cardinal Guido Del Mestri, Nuncio in Kenya, and Jean- Marie Gaëtan Ogez, Bishop of Mbarara in Uganda.
Emmanuel Kiwanuka Nsubuga ran from 1967 to 1975 the Episcopal Conference of Uganda. In 1976, Pope Paul VI. as cardinal priest with the titular church of Santa Maria Nuova in the College of Cardinals.
Emmanuel Kiwanuka Nsubuga put the management of the Archdiocese of Kampala in 1990 down for reasons of age. He died during a visit to the Federal Republic of Germany on April 20, 1991 in Cologne. He was buried in the Cathedral of Kampala.