In the fourteenth century, these views underwent a major change. William of Ockham, an Oxford Franciscan who died in 1349, attacked the Thomist view of compatibility between faith and reason. His view, widely accepted today, was that God must be accepted on faith alone; He could not be limited by human reason. Of course this view was not incorrect if one accepted the postulate of a limitless God versus limited human reasoning capability, but it virtually erased alchemy from practice in the fourteenth and fifteenth centuries. (Hollister p. 335)
Pope John XXII in the early 1300s issued an edict against alchemy, which effectively removed all church personnel from the practice of the Art. (Edwardes, p.49) The climate changes, Black plague, and increase in warfare and famine that characterized this century no doubt also served to hamper philosophical pursuits in general.
Nicholas Flamel had these mysterious alchemical symbols carved on his tomb in the Church of the Holy Innocents in Paris. Alchemy was kept alive by men such as Nicolas Flamel, who was noteworthy only because he was one of the few alchemists writing in those troubled times. Flamel lived from 1330 to 1417 and would serve as the archetype for the next phase of alchemy. He was not a religious scholar as were many of his predecessors, and his entire interest in the subject revolved around the pursuit of the philosopher's stone, which he is reputed to have found; his work spends a great deal of time describing the processes and reactions, but never actually gives the formula for carrying out the transmutations. Most of his work was aimed at gathering alchemical knowledge that had existed before him, especially as regarded the philosophers' stone. (Burckhardt pp.170-181)
Through the high middle ages (1300-1500) alchemists were much like Flamel: they concentrated on looking for the philosophers' stone and the elixir of youth, now believed to be separate things. Their cryptic allusions and symbolism led to wide variations in interpretation of the art. For example, many alchemists during this period interpreted the purification of the soul to mean the transmutation of lead into gold (in which they believed elemental mercury, or 'quicksilver', played a crucial role). These men were viewed as magicians and sorcerers by many, and were often persecuted for their practices. (Edwardes pp. 50-75)(Norton pp lxiii-lxvii)
One of these men who emerged at the beginning of the sixteenth century was named Heinrich Cornelius Agrippa. This alchemist believed himself to be a wizard and was capable of summoning spirits. His influence was negligible, but like Flamel, he produced writings which were referred to by alchemists of later years. Again like Flamel, he did much to change alchemy from a mystical philosophy to an occultist magic. He did keep alive the philosophies of the earlier alchemists, including experimental science, numerology, etc., but he added magic theory, which reinforced the idea of alchemy as an occultist belief. In spite of all this, Agrippa still considered himself a Christian, though his views often came into conflict with the church. (Edwardes p.56-9)(Wilson p.23-9)