The relation between critique and scientific knowledge has become a perilous conundrum. The precarity of this relation is conspicuous in recent ‘post-truth’ dynamics, but also in the field of Science and Technology Studies, where established critical approaches to scientific knowledge have been subject to devastating (self-)criticism. This article explores an aspect of critique often left unnoticed, namely that of doubt, asking whether it might provide a pathway for rethinking scientific reasoning and critical thinking. Drawing on ethnographic studies of a university-wide initiative to promote the integration of research and teaching, the article considers students’ and researchers’ ways of tackling doubt in processes of scientific inquiry and research. Contemplating what has been termed the positivity of doubt in American pragmatism, and its recent developments in French pragmatism, the paper considers the implications of these doubtful moments for how we might approach the cultivation of critique in and of scientific knowledge today.