This work aims to assess how regional innovation systems support research and innovation smart specialization strategies (RIS3) in coal intensive regions. Although many authors have analyzed energy transition paths for the European coal regions, no study has assessed how the network properties of their innovation systems are aligned with the priorities identified in their RIS3. This work fills this gap, relying on social network analysis (SNA) to assess innovation systems’ underlying networks, considering the active role of their nodes, thus, contributing to the innovation systems literature in the areas of modelling, simulation and performance evaluation. Within this work, regional innovation systems are modelled as research networks. These networks are promoted by the consortia funded by the European H2020 program. The assessment of the topology and properties of these networks enables the evaluation of the functioning of the innovation system, its technological strengths, as well as the key players involved. Based on these results, the characteristics of the innovation systems are compared to the priorities established by the RIS3. Three Spanish coal intensive regions (Aragón, Asturias and Castilla y León) are considered as use cases in this study. The obtained results indicate that, in some cases, the technological strengths of the regional innovation systems are not considered in the identification of the RIS3 priorities, while some RIS3 priorities are not supported by the innovation system. Considering these results, this paper proposes recommendations for regional and European policymakers, as well as for participants in the European research programs.