Climate and land cover changes are the two most important stressors causing the decline of amphibians’ populations worldwide. Within the Mediterranean area, one of the global biodiversity hotspots, the endemic Italian yellow-bellied toad ( Bombina pachypus ) suffered the same fate, as the decreases and local extinctions proved over time. Since the need to preserve this Apennine endemic species is evident, we take advantage of a novel approach combining climate-based ecological niche models and post-modelling GIS techniques (i.e., the weighted overlay framework) to produce finer species distribution models for B. pachypus . In doing so, we coupled climate variables with topographic-, hydrologic-, and habitat-related predictors, sharpening the potential species’ distribution at its whole range scale. Our findings show a latitudinal subdivision in predicted suitability: Central Apennines populations are expected to suffer more than the Northern ones, with considerable potential future losses of genetic diversity. On the contrary, Southern Apennines’ suitability is predicted to remain stable over time, preserving the vast diversity. When assessing the coverage that protected areas offer to the locations of suitable habitats for B. pachypus , the protected sites of the Central Apennines result in slightly less suitable conservation areas than those in the Northern and Southern Apennines. The overall protected areas coverage is currently low (∼20%) and predicted in the future to narrow towards medium suitability values, except in Southern Apennines, where an increase is inferred. In light of our spatially-explicit results, we suggest that a national-scale conservation strategy should consider different management options according to the sub-territories that our analyses highlighted. Our coupled “weighted modelling – spatialised genetic inference” approach permits us to support different conservation policies at all spatial scales, capitalising on relatively few input data. Also, in-depth spatial analyses should be performed to support effective protection strategies and management for the conservation stakeholders. • Fine-tuned SDMs deepen knowledge and strongly uphold Bombina pachypus conservation. • Changes will differently affect biogeographic sectors’ suitability for B. pachypus. • Protected areas’ policy should base on predicted local responses to future changes.