The main challenges faced by Europe for 2030 concern the achievement of 30% of protected marine surfaces, the improvement of connections between marine protected areas (MPAs), and especially, their more efficient management. The governance of MPAs is therefore called upon to strengthen its objectives, becoming part of a wider network of actors in dialogue with economic counterparts, addressing manifold interference and impacts, and ultimately strengthening biodiversity protection. This work explores the local dimension of MPAs’ governance through the opportunities offered by the Interreg MED TUNE UP project “Promoting multilevel governance for tuning up biodiversity protection in marine areas” (2019–2022), which commits to enhancing the effectiveness of MPAs in the Mediterranean, through the implementation of Environmental Contracts. Based on this experience, a two-fold analysis of multiple case studies has been developed, considering both the local and the European scale of regulations and governance chains. The results show that the MPA Contract is an effective tool to improve the governance of European MPAs and thus tackle the local responses to EU and national protection policies through a process of vertical and horizontal subsidiarity. The need for an interinstitutional dialogue to address the establishment of effective environmental governance and the enforcement of regulations affecting marine areas has been highlighted.