Balikuddembe was enrolled as a catechumen in the following year and along with Andrew Kaggwa, was baptized by Père Simon Lourdel M.Afr.

[4] From November 1882 to July 1885 the Catholic missionaries, for reasons of security, abandoned the Ugandan mission and re-located temporarily to the southern end of Lake Victoria.

Early in his reign, the new king began to crack down on Christian missionaries and converts in his country, and executed the British Anglican bishop James Hannington and his companions on October 29, 1885, ignoring Balikuddembe's pleas to spare the bishop.

Godfrey Muwonge attributes this to the influence of Mwanga's Katikkiro (Prime Minister) Mukasa, who sought to control the spread of Christianity in Buganda by eliminating its teachers.

[5] On 15 November 1885 Balikuddembe was taken to a place near the Nakivubo river where he was beheaded and his body thrown onto a pile of burning firewood.