Knowles served a curacy at St Peter-in-Thanet in Broadstairs, Kent from 1974 to 1979. From 1979 he was precentor and senior curate of Leeds Parish Church before moving to become precentor and a canon residentiary at Portsmouth Cathedral in 1981. He was also a chaplain during his time at the cathedral and held the post of chapter clerk from 1985 to 1987. He became the vicar of Leigh Park in 1987, additionally taking on the role of Rural Dean of Havant from 1990. He was appointed Archdeacon of Portsmouth in 1993 and held the post until 1999.
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]
On 11 January 2023, Knowles was installed as Acting Dean of Chichester [13] following the departure of Stephen Waine. The Diocese of Chichester had earlier announced that Knowles would take up the role until April 2023.[14]