The alchemical corpus came from the Muslim world and was introduced in europe around the 12th century, and parts of this corpus are constituted of ancient Greco-Roman text preserved trough translation. Why this is important ? Because at that time (12th century) Europe enter in what historian of sciences call the "scientific revolution", with for example the rise of the Medieval University which were under the autority of the pope. The knowledge at that time were "only" based on the learning ("Lectio") and the interpretative debate ( "Disputatio") of a large corpus of text composed of the work of famous religious figure (from the early christian age) and antic author (Aristotle for exemple). So with the rise of theses center of knowledge (validated by the pope) we can observe a multiplication of though system and apprehension reality. There are all taking place in the range of the corpus of autority, which are, i say it again, validated by the pope. Therefore the alchemical corpus constituted of antic text can not really be contested (at least if there not engaging directly against the bible or the christian vision in general). Thereby the pope never directcly condemned alchemy, which are "just" another interpretive system of the reality, from the corpus of autority (like for example : Stoïcism, Platonism, Pythagorism, Hermeticism). So alchemy were tolerated. Plus alchemist were often under the protection (= employed) by powerful people (king prince and so on) because they pursue material realization (gold transmutation, immortality). To conclude alchemy were never persecuted in his globality at medieval time, of course individual persecution happened, but the general condemnation of the alchemy take place much later.

Hope my english is clear, not a native speaker.

Can provide sources if requested but currently the librairy is closed during christmas period.