This study was aimed to identify intermediary organizations active in nature conservation initiatives by adopting a multi-level (ML) and network governance (NG) framework and using social network analysis (SNA). We identified 256 coordinating beneficiaries and 1090 associated beneficiaries connected through 8310 project relations and financed through the EU-funded LIFE Programme from 2014 to 2020. Our results evidence a central component of the network where organizations from Italy, Spain, and the United Kingdom play a central role. In contrast, peripheral components return a framework of partnerships mainly constituted by actors of the same country (68%). Moreover, the characterization by type of actor confirms the widespread implementation of a multi-level governance approach in LIFE-Nature (NAT) projects, evidencing the significant presence of non-governmental organizations and foundations, mainly at a national level, in nature conservation initiatives. Our findings reveal that the intermediary capacity of key actors should be further reinforced, particularly toward the promotion of transnational cooperation and cross-sector alliances, by encouraging the involvement of stakeholders operating at the ground level (i.e., provincial and municipal levels).