Abstract European‐wide crises have required extraordinary responses from the EU and its member states that affected its governance and legal framework as well as its legitimacy. The recent COVID‐19 pandemic spread across borders and involved multiple levels of government to mitigate its socio‐economic impact and facilitate a swift recovery. Whilst it is often suggested that the EU's political legitimacy does not primarily derive from its democratic accountability, the need for speedy decisions and the uncertainty of outcomes further favours executives and intergovernmental decision‐making. As legislatures and subnational governments are pushed to the back, European crisis governance created issues of accountability and transparency with repercussions for the effectiveness and efficacy of its policy measures. The Recovery and Resilience Facility (RRF) is a particularly interesting case to study the political legitimacy and the implications of crisis governance from a multilevel perspective. By analysing the RRF's input, output and throughput legitimacy, we will not only be able to draw conclusions about democratic accountability, good governance and problem‐solving capacities of European crisis governance but also about its impact on the relations between supranational, national and subnational institutions and levels of government. Understanding the shift of influence and the empowerment of actors during times of crisis will thus contribute to our knowledge about the wider trajectories of European integration.