Conflicts of conscience are all-too-common in a clinical context. And how one conceptualizes conscience arguably makes an important difference with respect to how we conceptualize those conflicts. One the one hand, if conscience is merely a cognitive capacity, then conflicts of conscience will merely be cognitive in nature and will, for example, centrally concern the conceptual compatibility of certain beliefs. On the other hand, if conscience is also an embodied capacity, then conflicts of conscience will also be bodily in nature and will, for example, also concern bodily well-being and related phenomena. Whether conscience is purely cognitive in nature or also embodied makes a difference, then, for how we understand and therefore aim to resolve conflicts of conscience in a clinical context. In this paper, I develop a rough reconceptualization of conscience as not merely a cognitive capacity but also as an embodied capacity for the purposes of better navigating conflicts of conscience in a clinical context. This goal comes together in three parts. I begin by overviewing the traditional concept of conscience as it has historically come down to us, emphasizing the overly cognitive characterization that this capacity has often received. I then explain what it would mean to reconceptualize conscience as an embodied capacity and highlight the role that guilt, understood as an embodied phenomenon, would play in conflicts of conscience as well. Finally, I explore how reconceptualizing conscience as an embodied capacity would imply a corresponding reconceptualization of conscientious objection and moral distress in a clinical context.