We will examine the basic features of the Metaphysics of Nature in the context of 17th Century Chemistry - influenced by Cartesian mechanism, Baconian empiricism, and supernaturalism. As a paradigmatic figure, we pay closer attention to Robert Boyle’s (1627-1691) concepts about chemistry. The line of argumentation is as follows: first, we will sketch what I mean by using the ambiguous term “metaphysics” (section 2). Section 3 is dedicated to arguing that empiricism according to Francis Bacon was not the exclusive methodological programme for chemists in the 17th Century. Section 4 explores the realm of metaphysics with respect to how scientists were dealing with occult entities. In Section 5 we will briefly demonstrate why Chemistry as a Science does not exclude the realm of supranaturalistic entities. Our main goal is to argue that the rise of early modern chemistry as a Science depended very much on its underlying Metaphysics. Moreover, the shifts from Alchemy to Chemistry are not – as it is often assumed – the result of abandoning the metaphysical.