Natural philosophy was often seen as a means of reading the “Book of Nature” written by God’s creative act, and therefore must be seen against the background of religion. Older commentary has examined how post-Reformation confessional divides affected the moral and spiritual project of “Physico-Theology.” Some intellectual historians have suggested that there was something that could be described as the confessionalization of early modern physics. Other intellectual historians have argued that the homogenizing pressure of confessionalization was much less successful, both in popular culture and in natural philosophy. This chapter aims to advance these controversies by contrasting general confessionalization claims with case studies that examine whether and how particular contents of natural philosophy were shaped by theological concerns specific to different Christian denominations. These case studies analyze the influence theories of special providence had on cosmology, the problems that doctrines of the Eucharist raised for matter theories, the persistence of moral interpretations of natural particulars in natural histories, and the methodological foundations of eclectic natural philosophies. The upshot of these considerations is that confessionalization led to a much lower degree of homogeneity in natural philosophy than has been supposed.