This article outlines the results from the research on primary and secondary school pupils' conceptualisation of microorganisms. It has been observed from the past few decades that one conceptual model is dominant, in which microorganisms are considered harmful, disease-causing and living in dirty environments. These misconceptions are only likely to be reinforced in a pandemic. Considering the different conceptual obstacles, microorganism education will be challenging in the coming years to instil in young people a scientific and balanced understanding of this group of organisms, which play an invaluable role in life on Earth.