A growing body of empirical evidence suggests that land use change, and the resulting decline in both the area and quality of natural habitats, contributes to an increased incidence of disease in humans. Despite calls to leverage conservation policy to address the burden of disease linked to ecosystem change, the potential benefits are unknown. Efficiently reducing the burden of infectious disease through land use policies and conservation initiatives is challenging because it requires balancing trade-offs that depend on ecological and socioeconomic factors. To assess some of these trade-offs, we developed a dynamic model of optimal land use when ecosystem change affects the overall incidence of infectious disease. We compared the net benefits and paths of optimal policy in which the increased cost of disease resulting from natural habitat loss is included in the optimization with a base case where it is ignored. We found that ignoring the linkage between habitat degradation and infectious disease incidence in the planner's problem reduces the net benefits of land management, such as conservation efforts, and results in significantly higher rates of infection and health costs.