Just as with Isaac Newton, Robert Boyle also was a long way from being the no-nonsense scientist disdainful of occult knowledge. Far from being the ultimate debunker of alchemy, as modern scientific historians would have you believe, he was a fervent practicioner of it.

In letters dated 1646 and 1647 he speaks repeatedly of a mysterious "Invisible College," that seems to be referring to some sort of Masonic society. He says in one letter that "the cornerstones of the Invisible or (as they term themselves) the Philosophical College, do now and then honor me with their company."

At the time he established himself at Oxford around 1654, his two closest friends were John Locke and Isaac Newton. He is said to have taught Newton the secrets of alchemy, and the two met regularly to discuss alchemy and study works on the subject. Boyle also wrote many letters with mysterious correspondents on the European continent, which dealt extensively with alchemy and alchemical experimentation. Some of them speak of Boyle's membership in a Hermetic secret society which included the duke of Savoy and Pierre du Moulin. This makes the conjecture that he may actually have been one of the Grand Masters of the Prieure de Sion at one time more plausible than it first seems.

Between 1675 and 1677 Boyle published two ambitious books on alchemical subjects: Incalescence of Quicksilver with Gold and A Historical Account of a Degradation of Gold. In 1689 he published an official notice that said that he would be unable to receive visitors on certain days he had set aside for alchemical experimentation. He explained that this experimentation was to

...comply with my former intention to leave a kind of Hermetic legacy to the studious disciples of that art and to deliver candidly in the annexed paper some processes, chemical and medical, that are less simple and plain than those barely luciferous ones that I have been wont to affect and of a more difficult and elaborate kind than those I have hitherto published and more of a kind to the noblest Hermetic secrets or as Helmont styles them, "arcana majora."

He says that he was, sadly, unfortunately unable to speak as plainly as he can about these matters, because, "in spite of my philanthropy, I was engaged to secrecy."

The annexed paper mentioned above was never found. It most likely passed into the hands of Isaac Newton. On his death in 1691 Newton and Locke inherited most of his papers and correspondence, as well as a mysterious "red powder" that figured prominently in many of his letters and notes on experiments in alchemy.