The unprecedented economic and health impacts of the COVID-19 pandemic have shown the global necessity of mitigating the underlying drivers of zoonotic spillover events, which occur at the human–wildlife and domesticated animal interface. Spillover events are associated to varying degrees with high habitat fragmentation, biodiversity loss through land use change, high livestock densities, agricultural inputs, and wildlife hunting—all facets of food systems. As such, the structure and characteristics of food systems can be considered key determinants of modern pandemic risks. This means that emerging infectious diseases should be more explicitly addressed in the discourse of food systems to mitigate the likelihood and impacts of spillover events. Here, we adopt a scenario framework to highlight the many connections among food systems, zoonotic diseases, and sustainability. We identify two overarching dimensions: the extent of land use for food production and the agricultural practices employed that shape four archetypal food systems, each with a distinct risk profile with respect to zoonotic spillovers and differing dimensions of sustainability. Prophylactic measures to curb the emergence of zoonotic diseases are therefore closely linked to diets and food policies. Future research directions should explore more closely how they impact the risk of spillover events.