Malaysia and the United Arab Emirates are home to wealthy minority groups with little or no access to public higher education. These countries share parallel trajectories of economic and educational growth, yet they have starkly different citizenship and educational policies that govern the diverse populations within their borders. The result in higher education has been differentiated systems whose contours are largely shaped by these ethnic divisions. Institutional prestige, student enrolment, and long-term sector stability are the areas most strongly influenced, although outcomes differ between Malaysia and the United Arab Emirates due to differing national policies on citizenship. A comparative, vertical analysis of student interviews, institutional curriculum, and government policies indicates that institutions and governments can mitigate the deleterious divisions in higher education related to ethnicity and citizenship. Government policies which withhold citizenship or higher education from a particular ethnic or class group, will, in the long run, decrease the stability of the education sector and reinforce the ethnic divisions within a country. Conversely, inter-ethnic collaboration within university programs has the potential to improve ethnic relations between groups, while inclusive notions of citizenship solidify the higher education sector.