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Abstract The dilution effect hypothesis posits that increasing biodiversity reduces infectious disease transmission. Here, we propose that habitat quality might modulate this negative biodiversity–disease relationship. Habitat may influence pathogen prevalence directly by affecting host traits like nutrition and immune response (we coined the term “habitat–disease relationship” to describe this phenomenon) or indirectly by changing host biodiversity (biodiversity–disease relationship). We used a path model to test the relative strength of links between habitat, biodiversity, and pathogen prevalence in a pollinator–virus system. High‐quality habitat metrics were directly associated with viral prevalence, providing evidence for a habitat–disease relationship. However, the strength and direction of specific habitat effects on viral prevalence varied based on the characteristics of the habitat, host, and pathogen. In general, more natural area and richness of land‐cover types were directly associated with increased viral prevalence, whereas greater floral density was associated with reduced viral prevalence. More natural habitat was also indirectly associated with reduced prevalence of two key viruses (black queen cell virus and deformed wing virus) via increased pollinator species richness, providing evidence for a habitat‐mediated dilution effect on viral prevalence. Biodiversity–disease relationships varied across viruses, with the prevalence of sacbrood virus not being associated with any habitat quality or pollinator community metrics. Across all viruses and hosts, habitat–disease and biodiversity–disease paths had effects of similar magnitude on viral prevalence. Therefore, habitat quality is a key driver of variation in pathogen prevalence among communities via both direct habitat–disease and indirect biodiversity–disease pathways, though the specific patterns varied among different viruses and host species. Critically, habitat–disease relationships could either contribute to or obscure dilution effects in natural systems depending on the relative strength and direction of the habitat–disease and biodiversity–disease pathways in that host–pathogen system. Therefore, habitat may be an important driver in the complex interactions between hosts and pathogens.