Current EU policies aim to support regional research, development, and innovation activities. The Cohesion Policy, implemented through Structural Funds (SFs) Operational Programmes, seeks to foster local level innovation. In parallel, universities have become important drivers of regional development through their ‘third mission’ driven by the different policy levels. This article investigates the tensions between the primary institutional logics of the university and the institutional logic of the SF programmes in peripheral regions as experienced by a multi-disciplinary university network from Finland. The findings from the case study reveal competing and co-evolving institutional logics of the two frameworks; university-led SF activities increase collaboration with local stakeholders, but the implementation of SF projects remains challenging (e.g. strict guidelines, higher education (HE) policies driving research excellence). Further investigation of these results in different regional contexts could provide new tools for managing the university third mission more efficiently, through SF programmes and beyond.