Effective conservation planning needs to consider the threats of cropland expansion to biodiversity. We used Myanmar as a case study to devise a modeling framework to identify which Key Biodiversity Areas (KBAs) are most vulnerable to cropland expansion in a context of increasingly resolved armed conflict. We studied 13 major crops with the potential to expand into KBAs. We used mixed-effects models and an agricultural versus forest rent framework to model current land use and conversion of forests to cropland for each crop. We found that the current cropland distribution is explained by higher agricultural value, lower transportation costs and lower elevation. We also found that protected areas and socio-political instability are effective in slowing down deforestation with conflicts in Myanmar damaging farmland and displacing farmers elsewhere. Under plausible economic development and socio-political stability scenarios, the models forecast 48.5% of land to be converted. We identified export crops such as maize, and pigeon pea as key deforestation drivers. This cropland expansion would pose a major threat to Myanmar's freshwater KBAs. We highlight the importance of considering rapid land-use transitions in the tropics to devise robust conservation plans.