A number of studies have investigated how the renewed interest in Plato's Timaeus led twelfth-century natural philosophers to take a growing interest in the material aspects of nature. By contrast, the implications of the resulting theories for the development of scientific knowledge have so far received but scant attention. But, as is shown in this paper, William of Conches, one of the most important natural philosophers of that age, not only broadened the material understanding of nature in his early text Philosophia, but also introduced a systematic distinction between the particular validity claims of philosophy and of physics. As we demonstrate, this distinction allowed for the formation of different disciplines, each having its particular methodology and explanatory force. Thus philosophy and physics could consider the same object, viz. the generation of the world, under the different and partly even contradictory perspectives of divine creation and the nature(s) of beings. This article analyzes the range of application of this distinction and its systematic consequences for the study of nature (e.g. the elements) as well as its importance for the elaboration of a theory of knowledge.