The events of 1560, the treaty of alliance with England against France, the commencement of the work of destruction of cathedrals and monasteries, and, finally, the death of the queen-regent, no doubt actuated Beaton in his resolve to quit the distracted kingdom.

On the 15 February 1574, Beaton's name appears at the head of the list of the Roman prelates and clergy declared outlaws and rebels by the Scottish Privy Council; but he nevertheless continued to enjoy in his exile the favour of the young king (James VI) who, about 1586, appointed him, as the late sovereign had done, ambassador at Paris.

His intimate association with the House of Guise had naturally led him to join with the League against Henry IV, and on its dissolution he was threatened with banishment; but by the intervention of Cardinals Bourbon and Sully and of the king himself, he was allowed to remain in France.

Perhaps the most remarkable testimony to the respect felt for his character in Scotland is to be found in the fact that in 1598, nearly forty years after the overthrow of the ancient Church, the archbishop was formally restored, by an act of the Scottish Parliament, to all his "heritages, honours, dignities, and benefices, notwithstanding that he has never acknowledged the religion professed within the realm".

A sounder estimate of his worth is that of his Protestant successor in the See of Glasgow, Spottiswoode, who describes him as "a man honourably disposed, faithful to his queen while she lived and to the king her son; a lover of his country, and liberal to all his countrymen".