[1] In 1899, he became vicar of Hooton Pagnell near Doncaster, where in 1902 he founded St Chad's Hostel to prepare men of limited means for entry to theological college.

[3] In 1906, Willoughby was appointed vicar of St John the Baptist, Stockton-on-Tees, where his Anglo-Catholic practices brought opposition from some parishioners.

In 1914, accusations were brought by parishioners to Handley Moule, Bishop of Durham, that Willoughby had been involved in homosexual activity; he was asked to resign or face a full enquiry.

Shortly afterwards an election for a new bishop was held among the clergy of the church, with Willoughby coming first and James Ingall Wedgwood second,[1] and on 28 October 1914 Willoughby was consecrated by Mathew, Bernard Mary Williams and John Briggs Seaton at the Royal Bell Hotel, Bromley, and given the title Auxiliary Bishop of St Pancras.

[5] Following his consecration, Willoughby published pamphlets entitled "The Conversion of Great Britain: What can the Ancient Catholic Church of England do?"