The Domesday Survey records that the large manor of 'Bodeltone' was held by Earl Edwin in 1066 and included 77 carucates; in 1086 it was held by the king. Around 1090 it was granted to Robert de Romille.
The priory was founded in 1120-1 at Embsay, NE of Skipton, on a site also at the margin of hill and lowland, but more exposed. The place is now occupied by the house called Embsay Kirk [Leach and Pevsner (2009), 246]. The foundation charter records the gift for a church of regular canons made by William Meschin and his wife Cecilia de Romile to Reynold, prior of the church of Holy Trinity at Skipton, along with the chapel of Carleton and the whole vill of Embsay. The community moved to Bolton c.1151 under the patronage of Alicia de Romilly, daughter of the founders: VCH II, 195; Burton (1999), 80-3. Richard Morris, in a lecture at the church in 2015, said that the unusual dedication may have come about through a family link to Durham priory: Ranulph Meschin, elder brother of William, was on the prayer list of the monks there.
To begin with, the canons seem to have made or taken over a church represented by the rougher walling in the W 2½ bays of the E arm. Around 1170-80 that building was extended eastward or was repaired: the crossing-piers were built and N and S transepts added with chapels on their E side, and the two plain archways were cut through the old walls. The S and N walls of the nave must have been begun at this time too, to support the crossing piers [Thompson (1928), 131]. The S nave wall would have been raised sufficiently to enable the cloister walls to be built around 1190 [Thompson (1928), 131-2]. The nave dates from 1240. The W tower to the nave was never completed.
After the Dissolution, the laity kept the nave of the church. The village is mostly, if not entirely, part of the Bolton Abbey Estate.