To develop effective public health management strategies, it is necessary to account for the viewpoints of all stakeholders. Thus, anthropological approaches can potentially inform strategies for preventing and managing zoonotic diseases. Here, we use Q fever as a starting point for exploring how small ruminant farmers perceive the reality of microbes by disentangling the farmers’ often subtle relationships with their livestock, disease, and the world in general. We found that livestock farmers feel like they exist in the borderlands between two worlds: the non-naturalistic World A, characterised by long timespans and complex relationships with non-humans, and the naturalistic World B, characterised by short timespans and the control of non-humans. The occurrence of diseases leads to tension and shifts between the worlds, depending on how much farmers entrust World B with health risk management and relations with non-humans. Significant or complete delegation of these responsibilities may result in a sense of unease and dispossession, particularly when World B fails to provide productive solutions. Whether farmers view Q fever as mysterious and threatening is also highly dependent on the degree of health risk delegation. Overall, the agent that causes Q fever is perceived in one of two ways: as a fearsome pathogen or a normal denizen in the farm’s ecosystem. These results have implications beyond Q fever and clearly illustrate the concept of the “microbial turn”, which emphasizes the plurality and ambivalence of the relationships between humans and microbes.