A pervasive, and still stubbornly persuasive, Enlightenment story holds that Isaac Newton’s 1687 Philosophiae naturalis principia mathematica played a decisive role in naturalizing early modern cosmology and physical science. Newton, however, was a committed, if heterodox Christian, and his new physics and astronomy depended crucially on a belief in God’s role as both the architect and ruling Pantokrator of the universe. Enlightenment naturalism, therefore, did not develop directly out of Newton’s Principia even if his new mathematical physics became a vehicle for disseminating it once a naturalist understanding of ‘Newtonianism’ had been forged by others. This chapter traces the genealogies that produced Newton and the cosmology of his Principia, along with the naturalizing alternative that contemporaries misleadingly called Enlightenment ‘Newtonianism’. It shows that while these had become entangled by 1800, their conjunction was a historical creation rather than an outcome determined directly by Newton or his science.