This church was part of an Augustinian priory. In the 16th century, King Henry VIII ordered the dissolution of the monasteries and the building became the main church of a parish that covered much of Snowdonia, including the summit of Snowdon!
It is believed that a Celtic clas (religious settlement) was founded here in the 7th century. When the monastic chronicler Gerallt Gymro (Giraldus Cambrensis) visited the place around 1216, it was still an independent community. Shortly after his visit, the church was remodeled for its new role as a priory church under the patronage of Lord Llywelyn Fawr (Llywelyn the Great), who is associated with the legend of the dog Gelert.
The priory was damaged by fire several times. According to the Monastic Wales website, legal proceedings were brought against the monastery in 1350 for failing to pay dues to the royal bailiffs. The prior argued that Prince Llywelyn ap Gruffudd had exempted the community in 1272, but the document presented as evidence turned out to be a forgery. The prior was briefly imprisoned. A later prior was ostracized for supporting Owain Glyndŵr's rebellion in the early 15th century.
The church was restored twice in the 19th century, but much of the medieval masonry remains, including some that probably predates the reconstruction around 1220–1230.