Conservation funds are grossly inadequate to address the plight of threatened species. Government and conservation organizations faced with the task of conserving threatened species desperately need simple strategies for allocating limited resources. The academic literature dedicated to systematic priority setting usually recommends ranking species on several criteria, including level of endangerment and metrics of species value such as evolutionary distinctiveness, ecological importance, and social significance. These approaches ignore 2 crucial factors: the cost of management and the likelihood that the management will succeed. These oversights will result in misallocation of scarce conservation resources and possibly unnecessary losses. We devised a project prioritization protocol (PPP) to optimize resource allocation among New Zealand's threatened-species projects, where costs, benefits (including species values), and the likelihood of management success were considered simultaneously. We compared the number of species managed and the expected benefits gained with 5 prioritization criteria: PPP with weightings based on species value; PPP with species weighted equally; management costs; species value; and threat status. We found that the rational use of cost and success information substantially increased the number of species managed, and prioritizing management projects according to species value or threat status in isolation was inefficient and resulted in fewer species managed. In addition, we found a clear trade-off between funding management of a greater number of the most cost-efficient and least risky projects and funding fewer projects to manage the species of higher value. Specifically, 11 of 32 species projects could be funded if projects were weighted by species value compared with 16 projects if projects were not weighted. This highlights the value of a transparent decision-making process, which enables a careful consideration of trade-offs. The use of PPP can substantially improve conservation outcomes for threatened species by increasing efficiency and ensuring transparency of management decisions.