In his Essay concerning Human Understanding, John Locke explicitly refers to Newton’s Philosophiae naturalis principia mathematica in laudatory but restrained terms: “Mr. Newton, in his never enough to be admired Book, has demonstrated several Propositions, which are so many new Truths, before unknown to the World, and are farther Advances in Mathematical Knowledge” (Essay, 4.7.3). The mathematica of the Principia are thus acknowledged. But what of philosophia naturalis? Locke maintains that natural philosophy, conceived as natural science (as opposed to natural history), would give us demonstrations of the necessary connection between the (ultimately, simple) ideas constitutive of our complex ideas of various natural kinds of substances (e.g., gold). Indeed Locke goes so far as to suggest that a completely adequate natural science would also realize (perhaps, per impossibile) the goal of transforming the corpuscularian hypothesis into knowledge by demonstrating the necessary connection between the ‘microstructure’ (primary qualities of insensible corpuscles) of a particular natural kind of substance (e.g., gold) and the ideas of secondary qualities constitutive of the complex idea of that kind of substance. Locke’s conclusion concerning the possibility of the development of a natural science thus conceived is pessimistic: In vain therefore shall we endeavor to discover by our Ideas, (the only true way of certain and universal knowledge,) what other Ideas are to be found constantly joined with that of our complex Idea of any Substance: since we neither know the real Constitution of the minute Parts, on which their Qualities do depend; not, did we know them could we discover any necessary connexion between them, and any of their Secondary Qualities: which is necessary to be done, before we can certainly know their necessary co-existence (Essay, 4.3.14). It is understandable that, with such a conception of the science of nature, Locke found little of it in Newton’s Principia. In this paper, I further explore what might, perhaps with some hyperbole, be termed Locke’s ‘disappointment’ with the Prinicipia as a contribution to natural science. In particular, I argue that Locke’s adherence to the idealist epistemology of the Way of Ideas entails that mathematics cannot lend its certainty as a scientia to natural philosophy. Consequently, he finds more mathematics than natural philosophy in the Principia.