Increasingly, attention is being given to the religious underpinnings of Francis Bacon’s project to reform natural philosophy. Within this discussion, however, his vital invocations of Jewish religion and culture have been ignored or represented as largely static and unproblematic, rather than understood in terms of contemporary cultural and theological struggles. In his utopia New Atlantis, Bacon draws on the dynamics of Christian-Jewish relations for several interrelated polemical purposes. One purpose is to imagine, not a complete sundering of science from religion as some past scholars have concluded but nevertheless a specific kind of division between these two spheres at the level of social organization. Another is to affirm such a qualified division of religion and science at the level of the relationship between God and nature; this division is specifically affirmed against the background of the contemporary upsurge of radical forms of millenarianism and messianism, alluded to in New Atlantis, which put the relationship between God, nature, and earthly political order under new scrutiny. These theologically and politically heretical developments are at the heart of Bacon’s most significant polemical purpose here: to defend his project against a set of vulnerabilities historically associated with natural philosophy’s reception by Christianity, vulnerabilities heightened by Bacon’s apocalyptic framework and its susceptibility to being paralleled with these disruptive eschatologies.