<p>The essence of the university manifests in its ontological design, which determines future goals and shapes processes and practices across all dimensions of the institution. In this paper, we argue that ontological design matters for universities, for fundamentally transforming institutions, enabling aspirations for decolonisation, and driving a more meaningful contribution to addressing the climate and Nature emergency. Drawing on a study across two South African universities that examined sustainability perceptions and practices in terms of integrated social and ecological justice, the paper interrogates three forms of ontological (re)design in universities – neoliberal policies, a capabilities and well-being orientation, and African ubuntu philosophy. The paper concludes that an ubuntu-capabilitarian ontological design that embeds ecological consciousness and values would steer universities towards an education that fosters pluriversal knowledges, embraces human, spiritual, and non-human interconnection, and embodies ethics of caring, sharing, and repairing. Ontological redesign in this direction could promote more radical transformation possibilities for universities to advance human and ecological flourishing.</p>