This paper explores the root causes and trajectories of ethnic conflict in Ethiopian universities between 2017 and 2019. Adopting a critical approach that focuses on structural, historical, and discursive factors I argue that university conflicts constitute a microcosm of wider social and political fractures that have characterised the Ethiopian nation-building project under the Ethiopian People’s Revolutionary Democratic Front (EPRDF). Ethnic conflict in universities must be understood against the unresolved contradictions of the “nationalities question” as it was initially framed by the student movement of the 1960s during the late Imperial period. The resulting tensions over the country’s nation-building project constitute the structural background against which present-day political crises that preclude the benefit of multi-nationalism and diversity in the country unfold. Elite discourse has produced opposing narratives of oppressed and oppressors, making ethnicity a defining trait of national and local politics at the expense of diversity. These trends have divided university students, and Ethiopian society more broadly, by producing a simplistic binary of victims and perpetrators among different ethnonationalist groups. The recent political liberalisation and the widening of the political space since 2018 have amplified these dynamics further. As result, universities have become a contested terrain, a microcosm of ethnic confrontation that hinders a political debate conducive to national dialogue. The paper concludes by calling for universities to initiate a critical pedagogy that involves debate, dialogue and deliberation to challenge the dominant public discourse relying on divisive ethnonationalist politics. This may help universities to become critical sites for new historical possibilities and the formation of subjectivities that transcend the enduring legacy of the 1960s university student radicalism.