In 1983, Willmott returned to the United Kingdom as rector of Ecton, Northamptonshire, and warden of the Peterborough diocesan retreat house at Ecton House. In addition to these positions, he became Diocesan Director of Ordinands and of Post-Ordination Training in 1986. He became a canon residentiary and precentor of Peterborough Cathedral in 1989 (remaining Diocesan Director of Ordinands and of Post-Ordination Training) until 1997, when he became a canon residentiary of Durham Cathedral and Archdeacon of Durham.
In January 2014, in an interim arrangement, Willmott was appointed to oversight of the Channel Islands (part of the Diocese of Winchester) following a breakdown of relations with the Bishop of Winchester over the handling of alleged abuse.[10] Willmott retired on 12 May 2019.[11] In retirement, he retains oversight of the Channel Islands and his commission as an honorary assistant bishop of the Diocese of Winchester.[3]