This study documents advances in EU energy policy integration in the period 2007–2009 as compared to the baseline situation, defined as transfer of competency over energy-policy decisions to the EU level. These advances are discussed in light of EU integration theory, with the issue-linking approach from international negotiation theory as cross-cutting approach. A clear conclusion is that intergovernmentalist theory cannot be refuted. In fact, observations underpin that this approach explains much of the changes observed. We saw clear indications of changes in preferences by key member state governments from the baseline situation, with clearer willingness for allowing EU level governance. Another conclusion is that the energy policy integration achieved cannot be understood without reference to EU-level institutions providing entrepreneurship so as to find equitable solutions for the member states. Supranational institutions, notably the European Commission, backed energy policy supranationalism more skillfully than what is observed in the baseline period. Hence, initial change in member-state preferences was a necessary but not sufficient condition for the stronger energy policy integration seen in the period. In order to investigate the broader legitimacy base among non-state stakeholders, the study applies the policy network approach. A main conclusion is that the preferences of major stakeholder networks were quite stable when compared to the baseline situation, although longer-term changes are observed. This said, we observed strong indications of shifts in opportunities of various stakeholder networks to influence Commission energy policy-making. A final conclusion is that the increments towards stronger EU integration were facilitated by the tactic of simultaneously negotiating different sub-policies, i.e. through issue-linking. The agreement reached thus represented higher ambitiousness than the baseline situation coupled with a stronger and broader legitimacy base. The study ends with a brief discussion of how robust the new-achieved legitimacy for EU energy policy integration really is, in light of deep economic crisis unfolding from 2007.