Despite the environmental benefits associated with wind energy, studies have confirmed the occurrence of significant levels of bat and bird fatalities at windfarms, which raise concerns about the long-term effects of these infra-structures on these populations. Reliable estimates of windfarm fatalities are fundamental for accurate environmental assessment studies and supporting management actions. A spatially explicit agent-based model (ABM) was developed to investigate how searcher “controlled” variables, i.e., different field monitoring protocols, monitoring periods and periodicities influence the success of carcasses detection in field trials and estimator accuracy. Different rates of bat mortality due to collision, scavenger pressures and habitat complexity were simulated in order to reproduce variable conditions that might take place at onshore wind facilities. Based on our findings we propose a reduction in the monitoring periods and a shortening in the periodicity of searches in order to reduce bias in the estimations and increase the confidence limits of impact assessments associated with mortality estimates at onshore windfarms.