I argue that Pierre Bayle was the first modern author to re-secularize the concept of moral conscience after it had been tied to Christian theology for centuries. Bayle’s first moral writings espoused a traditional, theological conception of conscience which was unfit to support his theory of toleration. Over three decades of reflection, Bayle gradually rendered conscience completely independent of theology, and therefore made it suitable as a foundation of a theory of universal toleration. We witness in Bayle’s moral writings not only the emergence of the modern, secular conscience, but also the process of secularization.