Religious debate
Through the influence of his talented and well-educated wife, Sarah Frances Bunyon, Colenso became one of only a handful of theologians to embrace Frederick Denison Maurice, who was raised a Unitarian but joined the Church of England to help it "purify and elevate the mind of the nation". Before his missionary career, Colenso's volume of sermons dedicated to Maurice signalled the critical approach he would later apply to biblical interpretation and the baleful impact on native Africans of colonial expansion in southern Africa.
Colenso first courted controversy with the publication in 1855 of his Remarks on the Proper Treatment of Polygamy, one of the most cogent Christian-based arguments for tolerance of polygamy.
Colenso's experiences in Natal informed his development as a religious thinker. In his commentary on St Paul's Epistle to the Romans (1861), he countered the doctrine of eternal punishment and the contention that Holy Communion was a condition to salvation. He also questioned the presence of a distinctly Christian Church in Rome, asking: "Was there, in fact, any Christian Church at Rome at all, at this time, distinct and definitely marked off from the Jewish community? There would seem to have been none whatever ..." Colenso, as a missionary, would not preach that the ancestors of newly Christianised Africans were condemned to eternal damnation.
The thought-provoking questions put to him by students at his missionary station encouraged him to re-examine the contents of the Pentateuch and the Book of Joshua and question whether certain sections of these books (e.g., Noah's Ark, the Deluge, the Crossing of the Red Sea, the Exodus, etc.), should be understood as literally or historically accurate. His conclusions, positive and negative, were published in a series of treatises on the Pentateuch and the Book of Joshua, from 1862 to 1879. The publication of these volumes created a scandal in England and were the cause of a number of counterblasts from those (clergy and laity alike) who refused to countenance the possibility of biblical fallibility. Colenso's work attracted the notice of biblical scholars on the continent such as Abraham Kuenen and played an important role in the development of Old Testament criticism in Britain; not only in relation to the theological/doctrinal issues of the Bible's inerrancy, infallibility, and literalism (rather than allegorism), and not only in relation to what many considered to be its scientific, historical, geographical, and chronological inaccuracies, and the consequent controversies about the age of the Earth, but, also, in relation to the precise accuracy of the translations-of-the-original presented in particular versions, as well as the separate question of how the Bible itself had developed — and which parts (when written, and by whom) of which particular texts (and in what order) should be included in the Bible itself.
Colenso's biblical criticism and his high-minded views about the treatment of African natives created a frenzy of alarm and opposition from the High Church party in South Africa and in England. As controversy raged in England, the South African bishops headed by Bishop Robert Gray pronounced Colenso's deposition in December 1863. Colenso, who had refused to appear before this tribunal otherwise than by sending a proxy protest (delivered by his friend Wilhelm Bleek), appealed to the Judicial Committee of the Privy Council in London. The Privy Council eventually decided that the Bishop of Cape Town had no coercive jurisdiction and no authority to interfere with the Bishop of Natal. In view of this finding that Gray's pronouncement had been made ultra vires, there need be no judicial opinion given upon the allegations of heresy made against Colenso. The first Lambeth Conference was convened in 1867 to address concerns raised by the Privy Council's decision in favour of Colenso.
His adversaries, though unable to remove him from his episcopal office, succeeded in restricting his ability to preach both in Natal and in England. Bishop Gray not only excommunicated him but consecrated a rival bishop (William Macrorie), who took the title of "Bishop of Maritzburg" (the latter a common name for Pietermaritzburg). The contributions of the missionary societies were withdrawn, but an attempt to deprive him of his episcopal income and the control of St Peter's Cathedral in Pietermaritzburg was frustrated by another court ruling. Colenso, encouraged by a handsome testimonial raised in England to which many clergymen had subscribed, returned to his diocese. A rival cathedral was built but it has long since been sold and moved. The new Cathedral of the Nativity, beside St Peter's, honours both Bishop Colenso and Bishop Macrorie in the names it has given to its halls.
Songs were written by Samuel John Stone as a response to the schism within the Church of South Africa. It inspired him to write a set of hymns titled Lyra Fidelium; Twelve Hymns on the Twelve Articles of the Apostles' Creed (1866). Among them was "The Church's One Foundation".