The European Union experienced several significant crises before the eruption of the COVID-19 pandemic that could result in paradigmatic changes that advance either the EU’s coordination or its disintegration. This paper investigates responses to the COVID-19 pandemic in Europe and explains the policy changes during the crisis using a comparative framework of neo-functionalism and intergovernmentalism in European integration theory. Tracking integration theories and comparing the new dynamics arising from the pandemic, we demonstrate that the pandemic has intensified long-standing trends in EU governance, resulting in the shift in EU governance during the pandemic being interpreted as both a reconceptualization of interests and a reframing of norms. The pandemic is therefore a wake-up call for the EU about the lack of deep European integration and incremental change, particularly with respect to the EU’s relative ineffectiveness in influencing its members’ health policies and reforms.