This article explores what it means to flourish in and through education and why we should position such flourishing as an issue of morality. We draw on the capabilities approach (CA) advanced by Amartya Sen and Martha Nussbaum and locate the argument in the practical context of higher education (HE) in unequal societies. We use qualitative data from year one of a three-year longitudinal study exploring student agency and well-being at a South African university to consider flourishing in and through education. Using the CA concepts of well-being, agency, practical reason and affiliation, we argue that the CA provides a philosophical grounding that takes account of both personal and relational flourishing and morality. Flourishing "in" education requires consideration of the well-being and agency of students. Flourishing "through" education draws attention to the role of education in promoting well-being and flourishing beyond its walls by fostering a social and moral consciousness among students.