We identified climatically stable areas of seasonally dry forests (SDFs) from Central Brazil through time and assessed the effectiveness of the current reserves network in representing these climatically stable areas, as well as areas of high suitability in the present or in the future only. We used an ensemble approach based on several methods for ecological niche modelling (ENMs) to obtain potential distributions 16 SDF’ species for past (last glacial maximum), present, and future (end of XXI century) climate scenarios. We then computed how many current Brazilian reserves matched both stable areas (suitable areas for all time periods), present and future geographical ranges alone for each species, in a multi-level gap analysis. We found range shifts due to climate changes for SDF’ species. Although the future geographical range and stable areas for all analyzed species matched at least with one reserve, many protected areas will lose importance in protecting suitable areas for species in the future. Moreover, the current Brazilian reserves cover only a small amount of their climatically stable areas. However, some reserves will be suitable for many SDF’ species (90%) at the same time, but climatically stable for only half of them. Our findings show that vegetation community from SDFs may persist in Brazilian territories until the end of XXI century, and challenges about long-term conservation of the SDFs may be partially reached with already existing Brazilian reserve network, however the reserves should be connected to permit habitat tracking.