The advowson of Monkton Farleigh was annexed to the Manor and was held by the Priory of Farleigh. During the 14th century, when the property of alien priories was often in the hands of the King, owing to the French wars, the rights of patronage were usually exercised by the Crown. The advowson was granted with the Manor in 1536 to Edward Seymour, Viscount Beauchamp, and passed from him to the Bishop of Salisbury. The king presented in 1639 and 1641. This may have been due to the fact that John Davenant, Bishop of Salisbury (1621-1641) fell into disgrace in 1631 owing to his Calvinism. When the lessee of the Manor was granted in 1661, the patronage was reserved for the bishop who thereafter always presented.
In 1291 the value of the Church of Farleigh was stated to be £5. In 1341 the Rector held a messuage and garden and 26 acres of glebe land and pasture worth 26s. 8d. In 1428 the church was valued at 100s. In 1535 the value was £8. 1s. 2d of which 1s. was paid annually to the Prior of Farleigh and 9s. 11d. in dues to the archdeacon.