Covid-19 highlights the inadequacy of EU governance cross-border challenges, especially transnational health challenges, supporting the call for a Health Union. Health policy remains a near-exclusive national competence whose budget was heavily impacted by EU-driven austerity, especially in Southern Europe. The work provides a comprehensive empirical assessment of the pandemic case evidencing the limits of the current governance framework and tabled reform proposals. The analysis contributes an extended understanding of the implications of the lack of an effective EU public health competence. We assess comparatively (austerity-induced) geographic heterogeneities in health-care preparedness, outbreak, crisis management and outcomes, delineating the extent to which inequalities remain in the absence of a Health Union. Findings evidence an empirically grounded case for sovereignty pooling in the core transnational domain of public health while providing a preliminary policy evaluation of the proposal for a Health Union.