For the past couple of years, the COVID-19 pandemic had an immense impact on lives of individuals and societies around the world. The main purpose of this study was to delineate Swedish middle school (10-12-year-old) pupils’ understanding of bacteria and virus thereby illustrating the impact of the pandemic at schools and in society. Data were collected by semistructured, individual interviews and by asking participants to draw images of bacteria and virus. Thematic coding and content analysis of children’s annotated drawings were used. The morphology of the microorganisms from the drawings was analyzed by the deductively induced themes shape, surface texture and internal feature. Viruses were frequently considered larger than bacteria, but it was also common to view them being similar in size. Interrelationships between bacteria and viruses were expressed like a hierarchy with a “superior” microorganism, and as bacteria could generate viruses. Pupils drew microorganisms as cell-like and never portrayed them as animals or with anthropomorphic features, as reported in earlier research. Metaphoric aspects of drawings of viruses were summarized as being “bacteriophage-like” or “corona-like”. A virus was considered to induce the more grievous disease. Pupils seldomly tethered a specific virus to a specific infectious disease, and often named both "corona". However, when they did so, virus was tethered to flu and COVID-19 and bacteria to cold and plague. One ostensible suggestion for learning improvement would be to pay more attention to differences between microorganisms and their liaison to specific infectious diseases. This liaison is suggested as an important concept for developing contagion literacy. Furthermore, we recommend pathogenic bacteria and viruses to be explicitly taught in biology education at middle school or earlier in balance with knowledge about essential microorganisms. Finally, we propose the measures above to be integrated into the biology education of teacher´s education.