There may well have been a church at Potton in Saxon times, but one of the first mentions of one is in 1094 when Simon de Senlis, Earl of Northampton granted St Mary's Church to St Andrew's Priory, Northampton. Before this the land was held by Countess Judith - the niece of William the Conqueror.

Thereafter, the priors of St Andrew's became Lords of Potton Rectoria, the manor in which the church lay, the incumbents being Rectors of the Parish. In 1394 the prior invested the abbess and convent of Minoresses of the Order of St Clare, outside Aldgate, London, with the advowson of the church, as well as that of St Swithin's chapel in the town (which was in existence in 1107), the prior retaining the rectorial rights as Lord of Potton Rectoria. After this event the next incumbent (in 1404) and his successors became Vicars of the parish.

The Dissolution of the monasteries in the 16th century saw great changes. Potton Rectoria (the Rectory manor) and the right of the rectorial tithes passed into the hands of the Crown. They were leased to various tenants and were sold in 1591 to Rowland Litton. After this the rectory manor and the 'right of tithes' passed by sale in different ways. The former passed into the ownership of several families, including the Burgoynes, Spencers and Whitbreads.

In 1917 Samuel Howard Whitbread sold all his manor lands in Potton at auction. The right of the rectorial tithes also passed through several hands and in 1698 it was purchased by Thaxted parish in Essex under a decree in Chancery and in pursuance of the will of William Lord Maynard. Trustees were appointed as 'rectors impropriate' (or lay rectors) who were, and still are, responsible for the upkeep of the fabric of the chancel of the church (a duty that may lapse if an Act of Parliament is passed to abolish lay rectorships). The advowson or right of presentation of the incumbent also passed to the Crown at the Dissolution and was retained. It is presently exercised by the Lord Chancellor as representative of the Crown.

The tithes, both rectorial and vicarial, were exchanged for allotments of land by an Act of Parliament in 1815. Tithe Farm (the allotment granted to the rectors impropriate) and Vicarage Farm (the vicar's allotment) were the main areas that followed this exchange, both having been subsequently sold off.

In October 1916 the vicar of Potton, The Rev R S Bagshaw was instituted at Cockayne Hatley as Rector, with dispensation to hold Potton Vicarage with Cockayne Rectory. In February 1931 the two beneficiaries were permanently united. In March 1973 the United Benefice was joined by Sutton, the incumbent thereafter becoming rector of the united benefices of Potton with Sutton and Cockayne Hatley.