In social groups, infection risk is not distributed evenly across individuals. Individual behaviour is a key source of variation in infection risk, yet its effects are difficult to separate from other factors (e.g., age). Here, we combine epidemiological experiments with chemical, transcriptomic, and automated behavioural analyses in clonal ant colonies, where behavioural individuality emerges among identical workers. We find that: (1) Caenorhabditis-related nematodes parasitise ant heads and affect their survival and physiology, (2) differences in infection emerge from behavioural variation alone, and reflect spatially-organised division of labour, (3) infections affect colony social organisation by causing infected workers to stay in the nest. By disproportionately infecting some workers and shifting their spatial distribution, infections reduce division of labour and increase spatial overlap between hosts, which should facilitate parasite transmission. Thus, division of labour, a defining feature of societies, not only shapes infection risk and distribution but is also modulated by parasites.