Since the launch of the Lisbon strategy in 2000, considerable efforts have been made at the European level to advance integration in higher education under two separate yet interlinked pillars: the European Higher Education Area (EHEA) and the European Research Area (ERA). Grounded in the principle of differentiated integration, the EHEA and ERA have represented important drivers in the construction of a single market for education, even though characterized by an uneven implementation, overcrowded priorities and interests, and significant limitations in two of their key overarching aims: mobility and the achievement of convergence around common values. More recently, the Covid19 pandemic further challenges higher education, with different dynamics at play regarding funding allocations, student and researcher mobility, and knowledge exchanges among European universities. Within this challenging context for the governance of European higher education, this paper explores a very recent initiative in the field of higher education, the European Universities Initiative (EUI) alliances. The EUI is characterised by a hybrid type of university collaboration based on transnational alliances linking education, research, and innovation. Using the lenses of differentiated integration, the paper discusses whether the EUI alliances can lead to a trajectory of “integration without supranationalisation” with (trans) national institutions as key actors driving the alliances.