Great Indian Bustard (GIB) is listed as Critically Endangered, with less than 250 individuals surviving in three fragmented populations. The species is under tremendous threat due to various anthropogenic pressures. Effective management and conservation of GIB requires a proper monitoring protocol, which we propose using an occupancy framework approach to detect changes in the species’ population. We used occupancy estimates from various landscape level surveys and simulated scenarios to evaluate the effectiveness of the proposed protocol. Our result showed there is >70% chance of detecting 100% change in the occupancy with 100 sampling sites and 10 temporal replicates. While with double sampling sites, the same change can be detected with 4–6 temporal replicates. In absence of a robust population estimation method, we argue for the use of occupancy as a surrogate to detect change in population as it provides better insights for rare elusive species such as GIB. Our proposed methodological framework is more precise than previous methods, which will help in evaluating efficacy of management interventions proposed and the implementation of species recovery plans.