Lanercost is a sizeable building and would be assumed to be home to a large number of canons. However there were probably only about fifteen in addition to the Prior and Sub Prior. Lanercost was a perpetual temptation to the Scots, and its position was also useful to English defending armies. In 1296 the Scots invaded the area and set fire to the cloister at Lanercost. Hexham to the east in Northumberland fared even worse: the church was burnt down and two hundred boys locked into their school and burnt alive. Lanercost was again attacked in 1297 soon after repairs had been completed. King Edward I was a visitor on three separate occasions: first in 1280, then in 1300 and again in 1306 when he fell ill and had to spend the winter there with a following of some 200 persons.

Lanercost was again raided and extensively damaged in 1346 by King David of Scotland. These frequent attacks impoverished the Priory and much of its land had to be sold off to pay for repairs.

At the Dissolution in 1536, the Canons were ejected and everything of value seized by the Crown. The building was bought by from the Crown by Sir Thomas Dacre, illegitimate son of a member of the Dacre family of nearby Naworth Castle. Objections to the Dissolution were dealt with by a letter which King Henry VIII wrote to the Duke of Norfolk telling him to hang without mercy any monk or canon making trouble. Sir Thomas Dacre turned Lanercost into a private house and began to live there in 1559. A parish church was created by blocking up the north aisle of the Priory nave but the rest of the building was allowed to decay and stone was taken from it for use on other buildings. In 1716 this branch of the Dacre family died out and Lanercost reverted to the Crown. In 1740 work was carried out to improve and enlarge the parish church in the nave, which is still in use today. The remains of the Priory are in the care of English Heritage.