Gassendi's metaphysics is intended to preserve traditional, common-sense intuitions about substance within a materialist ontology of body. He articulates an anti hylemorphist account of substance and a reductionist account of the qualities of inanimate bodies that rivals, and in many ways resembles, the one Descartes provides. Unlike Descartes, however, Gassendi attempts to preserve the substantiality and individuality of the plants and animals we interact with. Thus, he needs to answer the sort of questions about unity and identity over time that were traditionally answered by appeal to form.

He does so in the course of providing a natural philosophy rather than in anything devoted to metaphysics so called. Although most of Gassendi's contemporaries accorded a prominent place to a discipline they called metaphysics, the Syntagma moves from logic to physics to ethics, with no book on metaphysics at all. This is the standard Stoic and Epicurean ordering, so it is unsurprising that Gassendi adopted it.

Rejecting metaphysics as an independent branch of philosophy does not imply anything like a rejection of the sort of ontological questions typically taken to be central to metaphysics today. Nor does it involve a rejection of the sort of natural theological questions that Gassendi's contemporaries often understood as central to metaphysics. For instance, he treats topics such as the nature of providence, the various proofs of God's existence, and the immortality of the soul as part of his physics, thus integrating them into what he considers to be first philosophy (1.133b–4a).