On May 29, 1546, a party of sixteen men waited until the Cardinal's mistress, Marion Ogilvy, had departed by the postern gate in the early hours of the morning. Just after the first shift of masons and builders were beginning work on the castle fortifications, William Kirkcaldy, the Laird of Grange, approached a sentry and asked if the Cardinal was yet awake. The man became suspicious and was stabbed and tossed into the moat.

The conspirators, led by Norman and John Leslie, sons of the Earl of Rothes, hustled into the castle and showed out the workmen. By this time an alarm had been raised. Beaton and his page boy barricaded themselves in his bedroom with furniture, only to see smoke billowing under the door as the intruders applied a brazier of coals to it.

Beaton opened the door, pleading that they could not kill him since he was a priest. John Leslie and Peter Carmichael of Balmadie ignored his pleas and stabbed him with their 'whingers' (small daggers).

The third assassin, James Melville, sought to turn the act into an execution for the murder of his friend Wishart by calling on Beaton to repent before running him through twice. Beaton allegedly cried, 'I am a priest, fye, fye' before moaning, 'All is gone,' and expiring.

What followed is brutal. They hung the body outside the castle window for all to see, and the historian Pitscottie records that 'ane [one] called Guthrie pished [urinated] in his mouth.' The body was then salted and thrown into the 'bottle' dungeon, which had not long since housed Wishart.