[1] He served his curacy at St Andrew's Church, Haughton-le-Skerne in the Diocese of Durham from 1981 to 1985.

[2] In 1990, he moved to the Diocese of London, where he became team vicar of St. Leonard's, Shoreditch and St. John the Baptist, Hoxton.

[1] In 2002, Macnaughton moved to the Diocese of Oxford to become Team Rector of the Hambleden Valley Group, a multi-church benefice.

Then, from 2007 until his appointment as a bishop, he served as Chief of Staff to the Archbishop of York: first to John Sentamu then to Stephen Cottrell.

[3] He was scheduled to legally take the See of Repton, and be consecrated a bishop the Archbishop of Canterbury, Justin Welby, on 28 January 2021:[6] however, this was postponed due to the ongoing COVID-19 pandemic.