The EU aims for a global leadership role in the implementation of policies to combat climate change and to transition to a ‘clean’ energy system. While climate and energy policies represent areas of shared competence between the EU and its member states, the European Council and the Council of the European Union have often stood at the forefront of policy developments within these domains. In this paper, we ask how and why the roles of the European Council and Council have evolved in EU climate and energy policy. To do this, the paper proceeds in three steps. First, we review literature on ‘new intergovernmentalism’ and ‘intergovernmental union’ to develop our conceptual framework. Second, we examine how and when the member state institutions have initiated and blocked policy options. We trace changes in their roles over time by employing qualitative content analyses of Council and European Council conclusions, press releases, publications and speeches. We supplement this data with in-depth semi-structured interviews. Third, we confront the empirical data with factors from our theoretical framework based on ideas that the EU continues to experience deeper policy integration owing to increased member state coordination, but without increasing supranationalisation. We find that both institutions have exerted influence during the agenda setting, policy formulation and decision making stages of the policy cycle, but that the influence plays out differently for the Council and European Council. The paper contributes to understanding the (sometimes entrepreneurial) roles that the Council and European Council have played in driving or blocking policy. It provides a critical assessment of the appropriateness of ‘new intergovernmentalism’ as a lens to understand European integration through rich empirical investigation.