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Hegel’s and Schelling’s readings of Newton were decisive in their attempt to develop a “philosophy of nature,” and to characterize the relationship between philosophy and the natural sciences. This article traces how Hegel and Schelling begin with a shared belief that Newton unintentionally took a metaphysical stance, but differ in trying to explain why he did so and where it led him. Hegel thinks that Newton should have held on to his refusal of metaphysics. On the contrary, Schelling regrets that Newton was not more aware of the necessary connection between scientific concepts and metaphysical categories. It is argued that this divergence is rooted in a debate, started by Newton himself, over whether forces described by modern physics are real or conventional. It leads to a paradoxical conclusion: while Hegel promotes epistemological principles open to the work of the natural sciences, he takes a radical stance against the philosophical consequences of the scientific revolution initiated by Galileo and Newton. As for Schelling, he develops epistemological principles that are less favorable to the independence of the natural sciences, while advocating for a very modern conception of the structure of the universe, of physical forces, and of matter. The place of natural time in their respective systems can thus be clarified.