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In Metaphysical Foundations of Natural Science, the relationship between metaphysics and physics appears to be blurred by the amphibolic tone of Kant’s foreword. A study of three successive amphibolies of this kind enables us to introduce a new hypothesis: the issue of the specification of the categories featured in the system of principles of the first Critique must be taken into account in order to understand the relationship between the system of principles and the Metaphysical Foundations of Natural Science. As a result, two options are equally dismissed: 1) the principles and categories of transcendental philosophy are not mechanically applied to the study of nature; and 2) the Metaphysical Foundations of Natural Science are no arbitrary attempt to tailor Newtonian physics to the Kantian table of categories either. The connection between metaphysics and physics must instead be understood as a specification whose (modeling) modalities are shaped by systematic peculiarities of critical thought. The ambiguity of this relationship is eventually referred to the new framework of (mathematical) modeling that has been spreading in the natural sciences since the emergence of Newton’s paradigm. The Metaphysical Foundations can therefore be read as the metaphysical counterpart of physical modeling, thus bringing to light the implicit metaphysics of such a physical modeling.