The European Union and the world are challenged by the first pandemic for just over a century. While it has uncovered vulnerabilities in our social and economic systems, it has also provided new impetus, visibility and recognition of the critical role that health care systems and health professionals play in responding to the needs of people, serving society and underpinning the economy. It also underlined the power of research and innovation in uncovering the knowledge and developing the technologies to respond rapidly and effectively to public health emergencies. In addition to the direct suffering that COVID-19 is causing to symptomatic patients and their families, including long-term COVID-19 symptoms in survivors, the social distancing measures and lockdowns are causing major disruptions in social and economic life aggravating inequalities, loneliness and neglect, but also increasing existential fears, anxieties and distress, with serious negative impact on mental health and well-being. Population groups who are at risk of COVID-19, such as people suffering from co-morbidities and the elderly, are affected by these measures disproportionately but also young people entering and establishing their adult life. There is thus an urgent need for research and innovation to understand the long-term effects of both COVID-19 and the social distancing measures on people’s health and well-being, and in turn develop effective responses for a solid recovery of the European Union. Research conducted during the pandemic and following its sequels is pivotal to inform preparedness for potential similar events in the future. The pandemic has also demonstrated the downside of globalisation in which the dependence on global value chains can quickly result in shortages of critical supplies, such as essential medicines or other health technologies.