The Wars of Religion that followed the Reformation raised fundamental questions regarding citizens' competing religious, conscientious, and political obligations. In particular, Early Modern philosophers witnessed the potentially destabilizing nature of conscience-objections for legal and political order. In response, thinkers like Hobbes, Locke, and Rousseau reevaluated Medieval Christian epistemologies of conscience – what conscience means and what access to truth it gives to individuals – to make conscience "safe" for politics. These innovations had profound implications for both the epistemology of conscience and the freedom of conscience in modern political societies.First, I show how of all Early Modern political thinkers, Hobbes most clearly and radically identified the danger that individual conscience-claims pose for political stability and set the stage for Early Modern discourse on conscience. Next, I present Locke's solution to the problem identified by Hobbes, and demonstrate that Locke's advocacy of religious toleration and freedom of conscience rests on a fundamental shift in the epistemology of conscience and thus, for the relevancy of conscience for political life. Last, I argue that in contrast with Hobbes and Locke, Rousseau presents a much stronger – though no less modern – epistemology of conscience, while presenting the fundamental conflict between conscience and political society. What resulted from these thinkers are three distinct modern approaches to conscience which continue to influence the way liberal democracies understand and navigate conflicts between duties of conscience and duties of citizenship.