The main objective of this chapter is to present changes in the levels of innovation performance of the EU economies during the pandemic. This is realised by analysing the changes of the Global Innovation Index (GII) in 28 European Union countries in 2019 and 2022. The empirical research (including data visualisation, descriptive statistics and k-means clustering) has been performed in the R programming language. The results clearly show the time of the pandemic was in no way conducive to the growth of innovation in the economies. The mean GII for EU-28 in 2019 was 49.1, to decline to 46.09 in 2022. Twenty-five EU countries experienced falling GII in 2019–2022. Only 3 out of the 28 countries reviewed managed to slightly improve their innovativeness (France, Malta, and Estonia). The added value of this study consists in supplying data on the changes of innovation levels in the particular countries, tracking these changes in comparison with other countries, and identifying similarities (a division into clusters). This may provide valuable information to decision-makers in the individual countries when making informed decisions about innovation policies.