The 1560 Protestant Reformation devastated Whithorn. The church and monastery were suppressed, St Ninian’s shrine destroyed, and the cathedral stripped of its wealth and estates. By the late 1500s, the church lay in ruins.

Even before the Reformation, the cathedral priory experienced difficult times. Henry Madowell, the last genuine prior, died in 1514. After this Whithorn was held by commendators – secular administrators, who enjoyed the fruits but did not perform the duties of their office. There was also a disputed succession, arising from increasingly strained relations between Scotland and Rome.

In 1515, the Duke of Albany, governor of Scotland on behalf of the infant James V, nominated Alexander Stewart, his half-brother, to the position of commendator, but the Pope nominated an Italian cardinal.

In 1518, the Italian claimant renounced his title in favour of Gavin Dunbar. Dunbar was tutor to James V and was commendator of the priory until he became archbishop of Glasgow in 1524.

When Dunbar left, the cathedral priory entered the hands of the Fleming family. By now, Whithorn was treated as little more than a lordship – passed on in a noble family. By 1560 the number of monks had declined to around 16. By this time both canons and commendators had lost sight of the ideals of the order. Galloway’s bishop, Alexander Gordon, joined the Reformers. He reformed his diocese, persuading many of his clergy to join the Reformed church. Of 11 monks at Whithorn known to be alive in 1560, no fewer than seven became Reformed ministers or readers in Whithorn and the neighbouring parishes.