He became the vicar of Leigh Park in 1987, additionally taking on the role of Rural Dean of Havant from 1990.

[6] Knowles was installed as Dean of St Paul's Cathedral, London on 1 October 2007 after Letters Patent were issued on 20 September 2007.

[7] He resigned from St Paul's on 1 November 2011 as a result of the reactions to the Chapter's resolution to evict the Occupy London protesters from cathedral land.

[8] Knowles is also an honorary chaplain in the Royal Naval Reserve[9] and a patron of the Burgon Society.

[12] On 11 January 2023, Knowles was installed as Acting Dean of Chichester [13] following the departure of Stephen Waine.