Kabaka Mutesa I was known for his brutality and used the rivalries of the Anglicans, Roman Catholics and Muslims against each other to try to balance the influences of the powers that backed each group.

His successor, Kabaka Mwanga II, took a more aggressive approach by expelling missionaries and insisting Christian converts abandon their faith on pain of torture or death.

In 1885, three Anglican Ugandans were killed and the arriving Archbishop of the Province of Eastern Equatorial Africa, James Hannington, together with his party were arrested, detained and later executed at the orders of the Kabaka.

Joseph Mukasa, a Roman Catholic priest and an official of the Bugandan court, rebuked the deed and was arrested and beheaded.

This incident brought about the interference of Imperial British East Africa Company who backed a rebellion against Mwanga II by Christian and Muslim groups.

In 1913, the Bishop Tucker Theological College was established in Mukono and this institution was eventually expanded into what is now today the Uganda Christian University.

These radical proposals were opposed by the missionaries which resulted in a church hierarchy that was primarily expatriate until the independence of Uganda decades later.

Relationships between the Anglicans and Roman Catholics that have been strained since the fighting of 1892 saw a new turn with the establishment of Uganda Joint Christian Council.

In 1971, Idi Amin gained power in a coup d'état and was initially greeted with enthusiasm by the general population of Uganda.

The brutal and corrupt nature of the regime became evident soon and with the consecration of Janani Jakaliya Luwum as the new archbishop in 1974, the Anglican Church became more outspoken in opposition to the policies of Amin.

Bishop Ochola has however continued to be committed in working towards peace and reconciliation in northern Uganda[10] In 1980, Rwanda and Burundi were elevated to a separate province.

[19] In October 2009, the Ugandan Church's leadership reacted to the Vatican's proposed creation of personal ordinariates for disaffected traditionalist Anglicans by saying that although he welcomed ecumenical dialogue and shared moral theology with the Catholic Church, the current GAFCON structures already meet the spiritual and pastoral needs of conservative Anglicans in Africa.

[22] In 2022, Archbishop Kaziimba announced his support for the ordination of women to the episcopate and confirmed that a woman may be ordained a bishop in the Church of Uganda.