In this paper, we explore how participation in the strategic partnerships of the European University Alliances (EUAs) facilitates university capacity in regional development. The study utilizes the Quadruple Helix theoretical model and contributes to the literature on transnational university alliances in regional innovation ecosystems. A qualitative analysis of policy documents, media reports on EUA developments, alliance goals, and university implementation strategies is conducted within the context of Lithuanian higher education. In Lithuania's case, the primary rationale for participating in the EU initiative is both academic and economic. Furthermore, it is framed as addressing higher education challenges such as a low internationalization level, a mismatch between human capital and labour market needs, and the attractiveness of higher education. To achieve the strategic goals of the alliances, universities build networks including cross-sectoral linkages and engage in co-creation activities. The expanded and deepened interactions among different organizational spheres (helices) aim to foster innovation in national HE policy, strengthen university capacity through organizational innovation, and re-design teaching and research to drive social and economic transformations.