The COVID-19 pandemic had an immense impact on communities around the world. We know that new epidemic-prone diseases will emerge in the future. Consequently, it is important to investigate what impact the current pandemic had on school children’s understanding of infectious diseases in order to develop biology education based on that novel understanding. The aim of this study was to explore Swedish middle school (10-12-year-old) pupils’ understanding of infectious diseases and their perceived sources of knowledge. Data was collected through individual semi-structured interviews with fifteen pupils and analysed by thematic coding. Results revealed a great impact of the pandemic on the respondents’ conceptions. Firstly, their notion of infectious diseases based on their idea of COVID-19 was elusive because COVID-19 can manifest very differently. Secondly, the need to care about oneself and others was recognized. Thirdly, the importance of vaccines was recognized, but vaccines were given different roles. Finally, their understanding of infection seems to originate from informal domains such as the news and the Internet, rather than from biology education. One proposal for biology teaching could be to introduce scientific concepts earlier, to pay more attention to differences and similarities between infectious diseases, and to cooperate with other school subjects.