During a transitional period of Scottish history, responses to the French Revolution in the 1790s significantly affected Enlightenment intellectual culture across Scotland and, in particular, its existence in Edinburgh. The emergence of powerful counter-Enlightenment interests—championed by Henry Dundas—sought to censure the diffusion of ideas and values associated with France's revolution. In doing so, they targeted all controversial philosophical writings and liberal values for censorship and, in turn, gradually crippled the unique circumstances that had birthed the Scottish Enlightenment. Alarmed by the effect counter-Enlightenment policies had on Scottish intellectual culture, Dugald Stewart professor of moral philosophy at Edinburgh University (1785–1810) countered this threat with a system of moral education. His programme created a modern version of Thomas Reid's Common Sense philosophy whilst advancing that the best way to prevent the adoption of supposedly dangerous political and philosophical ideas was examining their errors. The tensions between counter-Enlightenment policies and Stewart's system of moral education erupted in the 1805 election of John Leslie as professor of mathematics at Edinburgh University, but the Leslie affair was not an isolated episode. This controversy embodied tensions over ecclesiastical politics in the Church of Scotland, national secular politics, and Scottish Enlightenment moral philosophy. At the same time, Stewart believed the Leslie affair would determine the fate of not only Edinburgh University but also the Scottish universities’ entwined relationship with Enlightenment. This article examines how Dugald Stewart's prominent role in the 1805 John Leslie affair pitted counter-Enlightenment interests against those of an emerging generation of the Scottish Enlightenment.