I’ve been searching for years for evidence about how much alchemists were bothered by the toxic substances they used. I have found nothing at all, and my notes contain a list of alchemical texts with comments like “Nothing mentioned”.
Sure, Chaucer wrote:
“And evermore, wherever they’ll be gone,
Men know them by their smell of foul brimstone3; for all the world they stink as does a goat;
Their savour is so rammish and so hot
That, though a man a mile away may be,
The odour will infect him, trust to me!

However that isn’t quite the same as a proper concern for ones life and awareness of the dangers, rather it shows that the alchemist and his clothes absorbed smells from the work itself.

Obviously it doesn’t help that I haven’t read all that many genuine medieval manuscripts or notebooks and many are in Latin or illegible handwriting. Nevertheless, I think it clear from what is available that, in general, the health effects of the materials alchemists worked with were either ignored, not known or simply passed on orally from master to apprentice. You would expect a certain knowledge of the bodily activities of substances when alchemists were physicians by trade and training. Agricola, in his book on mining mentions the dangers of lead once or twice, and he was a physician. But many other alchemists were not medical men and presumably wouldn’t know so much about the effects.
A different danger is mentioned by Thomas Charnock, who wrote that you have to be careful of your fire because many a man’s barn or house has been set on fire by accident.
And illustrations of alchemists often show the wearing of aprons, whether leather or wool or such is not clear, see for instance Breughel’s alchemist. ((Link or copy))

But that is it. So I was happy to find at least one mention of the dangers of alchemy, albeit from the 17th century. On page 97 of the paperback edition of “Alchemy tried in the Fire” by Principe and Newman, it says in note 11, that “Starkey’s friend Robert Child recounted later to Harlib that he had often warned Starkey that “he would ruine himselfe by using charcoale in places without chimneys, as also by the preparation of mercuriall & Antimonious medicines.” Child to Harlib, 2 February 1653.”

Thus we see an awareness that mercury and antimony compounds have an effect on humans, and that charcoal also has an effect. This latter would probably be from increased carbon monoxide from poorly burning charcoal not having a good escape from the room. Newmand and Princiep write that Robert Boyle encouraged Starkey to remove a pane of glass from the window of his laboratory in order to let fresh air in, but this then made his fires difficult to regulate, and the choice “seemed to be between controllable furnaces and breathing.” Of course mercuric and antimonial compouds had been used for centuries as medicines, which meant that they were known to affect humans, but alchemists just didn’t write it down.

Starkey probably learnt from this experience, because in a later work, under his pen name of Eirenaeus PPhilophonus Philalethes he wrote:
“Nor let they room be so …
… that the fumes rising
From Coals no vent may finde, for thou maist get
(as some have done, hereol less care devising)
Thereby such harm, which late thou wilt repent,
Hazarding life by their most hurtful scence.”