Cerrado is considered one of the world’s most threatened and floristically diverse tropical savannas. Distribution of the Cerrado flora comprises three countries: Bolivia, Brazil, and Paraguay; consequently, opportunities to conserve it require a transboundary effort. We aimed to (i) explore the relationship between a representative portion of Cerrado flora (8611 species), natural cover loss, and three country boundaries; and (ii) identify priority areas to expand protected areas at national and transboundary levels considering the different species conservation status, countries’ governance, and natural cover loss. We modeled the distribution of Cerrado species for the three countries and overlapped species ranges with country boundaries to calculate species ranges shared between countries and the degree of endemicity. We identified national and transboundary priority regions to expand protected areas. We found that the areas with the highest plant richness are distributed in the central part of the Cerrado and Campos Rupestres Mountain Savanna ecoregions in Brazil (>8500 for the whole country). Bolivia ranked second in species richness (>4300), followed by Paraguay (>3700). The most anthropized areas in Brazil overlapped with regions predicted to foster the highest biodiversity. Conversely, such patterns were opposite in Bolivia and Paraguay, which harbored regions with high opportunities for Cerrado flora conservation. Transboundary prioritization suggested slightly higher species protection, including threatened and endemic species. Restoring some regions primarily in Brazil will be necessary to protect 30 % or 50 % of the study area. Together, the three countries can support more comprehensive conservation actions for the great diversity of the Cerrado flora.