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Abstract Ensuring wind energy development does not cause biodiversity loss is a global priority. Wind turbines kill large numbers of bats, raising concern that global expansion of wind energy increases the threat of extinction of vulnerable bat species. Uncertainty about bat population size and status has hindered efforts to implement regulatory policies based on solutions known to reduce bat fatalities at wind energy facilities, in large part because the amount of fatality reduction necessary to protect bats has been difficult to define. Adoption of the full mitigation hierarchy for bats is urgently needed, including informed siting to avoid impacts to bats, minimization of bat fatalities using fatality thresholds to set operational conditions (e.g. curtailment) and compensation through offsets. We introduce a method to adapt the use of potential biological removal (PBR) to establish bat fatality thresholds at a project scale even with high uncertainty about bat populations. We propose a decision framework using fatality thresholds to inform turbine operating constraints that will lower the risk of unsustainable mortality and provide better financial forecasting for developers during project planning. Our fatality threshold calculation tool incorporates modified principles of PBR, general bat reproductive biology, IUCN status, local bat ecology, and facility area to define fatality thresholds for individual wind facilities. We use IUCN status and foraging guild to set initial exposure reduction targets and operational constraints meant to lower fatalities to meet thresholds. Adaptive management based on post‐construction fatality monitoring can then determine whether curtailment is sufficient to meet a fatality threshold or needs adjusting. Our proposed approach allows for high uncertainty about local bat populations but can incorporate new information that becomes available. Data defining local bat population density, seasonal variation in bat activity, or changes in IUCN status can be used to update fatality thresholds and operating regimes. Practical implication . Defining fatality thresholds to inform mitigation implementation should reduce bat fatalities, ideally to sustainable levels, while providing a measure of success for wind companies to ensure equitable regulatory conditions and help drive innovation for technology to reduce bat fatalities while maintaining or improving energy production capabilities.