During the forty years prior to the Reformation the abbey enjoyed the protection of the Earl of Carrick, two eminent members of the family being about that time abbots in succession to each other. At this period the right of appointment to vacant benefices was gradually passing into the hands of the Crown, and by 1550 that change was completed. In those troublous times the Church was felt to be in danger, and Abbot William Kennedy, who had acted as guardian to the young Earl Cassilis, who was then abroad, wrote to him to return to Scotland to look after the interests of the abbey. At the same time the Archbishop of Glasgow sent all his possessions to Crosraguel, as to a place of safety. These consisted of embroidered vestments, gold and silver plate, jewels, and a library of books of great value. Abbot William was succeeded by his nephew, Quintin Kennedy (1547-64), an ardent champion of the Church, whose contest with Knox at Maybole in 1562 is well known. It is thought that he was the first abbot to occupy the abbots’ tower, a fortified pele which stands at the south-east corner of the grounds. Gilbert M‘Brayar, one of the monks, is said to have made many “sumptuous additions” to the monastery. These were probably domestic structures in the cloister, whose ruins are still traceable. In 1561 an Act was passed by the Privy Council suppressing “Idolatori and all monumentis thairof,” and Arran, Glencairn, and Argyle were despatched to the West to carry the Act into execution. Amongst the other demolitions executed by them was the casting down of part of Crosraguel. Ten years before the Reformation leases of church lands were frequently granted to nobles and other powerful individuals who were able to protect them. Thus, in 1564, the whole benefice of Crosraguel was leased to the Earl of Cassillis for 700 marks (£466, 13s. 4d.) Under his protection the monks continued to occupy the monastery till 1592, probably later than any other abbey in Scotland. In 1570 occurred the famous “roasting of the abbot.” The Earl of Cassillis had resolved to get the whole property of the abbey into his hands, and endeavoured, by torturing Allan Stewart, the abbot, to force him to surrender the titles of the lands of the abbey, and he thus succeeded, in consideration of a large sum, in becoming sole proprietor of the regality. The abbot survived, but was maimed for life. He disposed of every shred of the monastic property, and died in 1587. The annexation to the Crown took place the same year. The possessions had been gradually disposed of by Queen Mary and her son to numerous retainers. George Buchanan received a pension out of the revenues, and King James intended to restore the abbey as a residence for his son Henry.