At the time of the 1572 St. Bartholomew's Day Massacre in Paris, Adamson had been living under cover at a tavern in Bourges for seven months; its aged landlord was later reportedly thrown from the roof for offering charity to such a "heretic".

During these turbulent political times, he took refuge in St Andrews Castle, where a so-called "wise woman", Alison Pearson,[5] who was later burned for witchcraft, cured his apparent "serious illness".

[3] In 1583, Adamson returned to public service by being posted as Scottish ambassador to the Court of St James's of Elizabeth I of England; whilst in London rumours were spread about his bad behaviour.

On his return he implemented strong measures in parliament against Presbyterians, and consequently accusations of heresy followed with excommunication at a provincial synod held at St Andrews in April 1586; however, at the next General Assembly this verdict was rescinded as being ultra vires.

His collected works, prefaced by a favourable panegyric, in the course of which it is said that "he was a miracle of nature, and rather seemed to be the immediate production of God Almighty than born of a woman", were published by his son-in-law, Thomas Wilson, in 1619.