During his time at Oxford he married Frances Mary, third daughter of Sir Charles Anderson, baronet (1804–1891) on 23 June 1863, and subsequently, his attitude to his work and life became more serious, proceeding MA in 1867 and going to train for the ministry at Cuddesdon College, then under Edward King.

His father ordained him deacon in December 1864 and priest in 1865 and, after short curacies at Cuddesdon itself and at Lea, was presented to living at Middleton Stoney, near Bicester, in 1868, though he had to resign from it two years later due to Frances' poor health (she died in October 1870 in San Remo of tuberculosis).

He was translated to Chichester on 16 January 1896, however, his health had been affected by his unflagging work in Newcastle, though there he found a number of ritualistic Anglican churches on the Sussex coast under fire from evangelicals from 1898 onwards.

This culminated in a judgment from Lambeth against the use of incense and processional lights in 1899, with which Wilberforce persuaded five of the nine ritualist incumbents in Chichester diocese to comply.

Attempting to protect the four others from prosecution and defending their work in the evidence he gave as a witness in front of the 1905 royal commission on ecclesiastical discipline (at which he also brought criticism to bear on what he saw as the evangelicals' prejudice and inaccurate claims), he tried to avoid the division and rancorousness he saw as results of the Public Worship Regulation Act 1874 and ensuing imprisonments and legal proceedings, despite having little personal investment in ritualism.