The European Commission's flagship European Universities Initiative (EUI) announced in 2017 laid out a novel regional approach to internationalisation by promoting the establishment of integrated transnational networks of universities, or alliances. Launched in consecutive pilot rounds, the EUI provided a fixed-sum grant to each alliance with the expectation that participating institutions and national governments co-fund their activities. Given the hierarchical structure of the European higher education space and varying national support for the Initiative, capacities of institutions to participate appear both unequal and exclusionary. This study draws on documentary evidence and interviews with EUI alliance representatives, exploring accounts from three distinct alliances from the 2019 pilot round. With nuances between the examined cases, it argues that the design of the EUI, intended as a vehicle for enhancing cooperation and excellence, intensifies vertical stratification of European higher education by supporting relatively advantaged institutions with respect to international partnership opportunities and resources.