In this essay, I examine Robert Boyle's strategies for making imperceptible entities accessible to the senses. It is well known that, in his natural philosophy, Boyle confronted the challenge of making imperceptible particles of matter into objects of sensory experience. It has never been noted, however, that Boyle confronted a strikingly similar challenge in his natural theology – he needed to make an equally imperceptible God accessible to the senses. Taking this symmetrical difficulty as my starting point, I propose a new approach to thinking about the interconnections between Boyle's natural philosophy and natural theology. For the most part, studies of science and religion in the early modern period work by seeking out the influence of explicitly stated religious beliefs on scientific ideas. I argue, by contrast, that we need to focus on Boyle's representational practices, using his attempts to represent imperceptible entities as a means of uncovering metaphysical and theological presuppositions that he did not always articulate when stating his religious beliefs. With new interpretations of both A Discourse of Things Above Reason (1681) and Some Physico-Theological Considerations about the Possibility of the Resurrection (1675), I show that there were crucial similarities between Boyle's practices for representing both God and atoms. I go on to show, moreover, that Boyle used these practices to enact an ontological stance at odds with one of his most important professed beliefs.