Addressing risks and pandemics at a country level is a complex task that requires transdisciplinary approaches. The paper aims to identify groups of the European Union countries characterized by a similar COVID-19 Resilience Index (CRI). Developed in the paper CRI index reflects the countries’ COVID-19 risk and their readiness for a crisis situation, including a pandemic. Moreover, the study detects the factors that significantly differentiate the distinguished groups. According to our research, Bulgaria, Hungary, Malta, and Poland have the lowest COVID-19 Resilience Index score, with Croatia, Greece, Czechia, and Slovakia following close. At the same time, Ireland and Scandinavian countries occupy the top of the leader board, followed by Luxemburg. The Kruskal-Wallis test results indicate four COVID-19 risk indicators that significantly differentiate the countries in the first year of the COVID-19 pandemic. Among the significant factors are not only COVID-19-related factors, i.e., the changes in residential human mobility, the stringency of anti-COVID-19 policy, but also strictly environmental factors, namely pollution and material footprint. It indicates that the most critical global environmental issues might be crucial in the phase of a future pandemic. Moreover, we detect eight readiness factors that significantly differentiate the analysed country groups. Among the significant factors are the economic indicators such as GDP per capita and labour markets, the governance indicators such as Rule of Law, Access to Information, Implementation and Adaptability measures, and social indicators such as Tertiary Attainment and Research, Innovation, and Infrastructure.