This chapter surveys prominent aspects of historical relations between theology and science in the early modern period. It argues that the medieval “handmaiden tradition,” in which natural philosophy was seen as a support to theology, continued throughout the period but with apologetic complications caused by the fragmentation of religious authority, and the proliferation of alternative new philosophies. It considers the mechanical philosophy and the concomitant concept of laws of nature, and their impact on mind-body dualism, and the development of natural theology. It also considers the role of natural philosophy in the rise of atheism, arguing that it did not create atheists, but was appropriated by them. Devout natural philosophers played into the hands of atheists by arguing among themselves as to the best way to combat atheism, and by taking a naturalistic line in their arguments, relegating God to the role of a remote primary cause and increasingly denying Providence. Finally, it considers persistent suggestions that Protestantism played a greater role in the promotion of the natural sciences than Catholicism. We consider here claims about millennialism as a stimulus to science; the effect of Protestant attitudes to the Bible and how it should be read,; and the role of Augustinian post-lapsarian anthropology.