The selection of priority areas for nature conservation must balance the costs and benefits of conserving biodiversity, protecting ecosystem services, and permitting human activities or resource use. In this study, we selected priority areas for conservation in a seasonally dry tropical forest in Brazil and analyzed changes in the protection of ecosystem services and the conservation of plant biodiversity upon excluding areas with high opportunity costs (e.g., where income would be lost if natural areas were protected) and high population density. We identified two types of protected areas: sustainable use (SU) and strict protection (SP). Plant biodiversity (181 species) and supporting services (water balance, net primary productivity, and soil fertility) were used to determine the optimal locations of both types of protected areas. Provisioning services (water supply, fodder, and genetic resources) were used to determine SU priority areas, while regulating services (water purification, carbon storage, and erosion prevention) were used to determine SP areas. The selection of lowly populated or costly areas was associated with a small decrease in the representation of biodiversity (4% loss in SP and 6% loss in SU) and a large decrease in the representation of supporting (36% loss in SP and 31% loss in SU), regulating (41% loss in SP), and provisioning services (7% loss in SU). Our results reveal that selecting priority areas with low population density and low opportunity costs would decrease the overall representation of ecosystem services in protected areas but would still improve the cost efficiency of biodiversity conservation efforts.