Calls for threat management actions to protect biodiversity and restore ecosystem function are rarely coupled with costed and prioritized sets of management actions for use in decision making. We present a cost-effectiveness approach for prioritizing threat management to maximize the in situ protection of biodiversity per dollar spent. The approach draws on empirical data and expert knowledge of major threats to biodiversity, feasible threat management actions, and likely responses of biodiversity to a set of costed management scenarios. An application assessing 637 vertebrate wildlife species in the Kimberley region of north-western Australia suggests that the likely functional loss of 45 mammals, birds, and reptiles over the next 20 years can be averted by effectively managing fire, grazing, and invasive species for approximately AU$40 million per year. Our approach is flexible and may be useful for delivering transparent guidance for conserving species and ecosystems in other regions, including those where data is limited.