Debate over balancing agricultural production and biodiversity conservation has generated two opposing strategies: a “land sparing” approach involving large-scale nature reserves, versus a “land sharing” approach where agricultural areas support wildlife through fine-scale conservation. As a result of this debate, studies focus almost exclusively on species diversity and food production, while ignoring other critical ecosystem processes such as disease dynamics. Here we quantify how tropical avian malaria in an abundant sedentary bird species responds at fine spatial scales in a “land sharing” system. We find the proportion and configuration of countryside forest elements within a radius of 400 m, proximity to the nearest river, and habitat type explains malaria prevalence across the region. We simulate “land sparing” and “land sharing” land use strategies and model malaria prevalence to find that land sharing mitigates malaria prevalence more effectively. With these analyses, we gain a better understanding of how biodiversity, ecosystem services, agricultural yield, and human well-being intersect in complex ecosystems.