In the debate about the impact of the eurozone crisis on the EU’s institutional balance, antagonists have often argued past each other. Supporters of the new intergovernmentalism contend that the European Council has supplanted the European Commission in policy leadership, while scholars who hold that the EU executive has been a winner of the crisis highlight the new management functions it has acquired. This article argues, first, that an accurate assessment of the institutional balance requires a more global evaluation of the Commission, acknowledging external and internal dynamics. Second, it contends that the crisis did not cause a Commission retreat but accelerated a process already underway that finds its origins in the presidentialisation of policy control. The adoption of fewer legislative proposals during the crisis was due to the ability and choice of a strong president to focus the attention on crisis-related areas. The broader lesson is that rather than marking a further step in the decline of the Commission, the crisis reveals how the centralisation of power within the institution and its expanded management duties have enhanced its capacity to take strategic action. The Commission’s role as an engine of integration will therefore endure, but in a different guise.