Conservation budgets are limited, requiring strategic prioritization among actions to efficiently protect species. Systematic prioritization approaches typically determine locations for conservation that most effectively balance species protection with cost. Proxies for cost are frequently used in prioritizing land for protection. Here, we combine financial cost estimates for private land acquisition and species habitat models into a spatial prioritization to explore cost-effective habitat protection, using a case study of species at risk in Ontario, Canada. Our findings suggest a key trade-off, whereby protecting the areas with the greatest concentration of species at risk may not be the best strategy for protecting these species. Instead, protecting species at risk may be most cost effective in areas where species-at-risk richness is still relatively high, but land costs are relatively low, such as in central Ontario. However, the budget required to adequately protect species at risk through land purchase would be much larger than is currently available for conservation efforts, even if public lands are preferentially protected. Therefore, to effectively protect all species at risk in Ontario, we recommend the use of alternative conservation measures, such as easements and incentives for restoration on private land, to supplement already protected areas.