In 1537 the Canons were ejected despite appeals by the people of the area, and four of them were hanged, as were 10 farmers who had supported them. The whole of the Priory's property was taken by the Crown: as usually happened the lead was stripped of the roof, to speed up the decay of the building. It would also have been normal for the stone to be taken from the walls for use on other buildings, but the Priory survived thanks to its founder, William Marshall, who 350 years earlier had made sure that an alter within the Priory be given to the people of Cartmel village and a priest provided for them. The village of Cartmel appealed to the Crown to be allowed to continue worshipping at the Priory and this was granted.

Until 1618 the villagers attended services in the choir while the rain came through where the roof of the nave had once been. Considerable financial help was provided for the restoration of the roof in 1618 by George Preston of nearby Holker Hall.

At that time the Priory and its surrounding buildings were considerably larger than the remains seen today. Stone from most its buildings was used in the construction of the picturesque village of Cartmel. The Priory Gatehouse survives in the village square and illustrates the impact the original range of buildings must have had on the visitor.

In 1643 some of Cromwell's 'Roundhead' troops stayed overnight in the village, stabling their horses in the church. The troops did some damage here as they did in most places they occupied: bullet holes can be seen in the door in the SW corner of the nave.

By 1830 the church was in need of repair and a long period of "restoration" began. Victorian restoration techniques were enthusiastic rather than sympathetic, but the decay of the fabric of the building was halted. Both the Priory and the charming village of Cartmel are well worth visiting.