The earliest written record of the parish church is from 1221, when the Abbess of the Benedictine Elstow Abbey in Bedfordshire disputed with a later Richard de Camville which one of them held the advowson of the parish. The Abbey won, and retained the right until its dissolution in 1539. After this the Crown held the advowson until 1608, when it was sold to Sir Henry Fowkes who immediately sold it on to Corpus Christi College, Oxford.

The Fermors were recusants and with their support the majority of Godington parishioners remained Roman Catholic. In 1739 Roman Catholics still outnumbered Anglicans in the parish, and a Roman Catholic priest lived in the parish to serve them. Early in the 19th century it was recorded that the farming families were Catholic but their labourers were Protestant. Until 1900 in the roof of the farmhouse at Moat Farm there was a Roman Catholic chapel that was served by a priest from Hethe. In 1759 it was also recorded that recusants from Godington worshipped at the Fermor family chapel at Tusmore Park.

By 1790 the mediaeval Church of England parish church of the Holy Trinity was in disrepair and in danger of collapse, and in 1792 William Fermor employed a fellow-Roman Catholic to rebuild it. In 1852 the church was restored and rectangular Georgian windows were converted to lancets, and in 1905 the building was restored again. The mediaeval font survives and some mediaeval masonry remains in the bell tower. The tower used to have three bells, but in 1792 two of them were sold to pay for rebuilding the church. The surviving bell was cast in 1717, and there is also a Sanctus bell cast in 1793.