Climate refuges have been used by several species over historical climate change. Ectothermic species often display good models for climate change studies because they are highly sensitive to temperature. Analysis of species loss with ecosystem and evolutionary values helps to understand environmental processes and climate change consequences. We determined the functional and phylogenetic diversity of amphibians in the Atlantic Forest hotspot, using multiple models representing present and future conditions. Through a novel approach, we predict species’ threat status by 2080, following the IUCN’s criterion B1. Our results estimate a drastic reduction in species richness, ecosystem functioning and evolutionary history at low latitudes and altitudes. We show that species will tend to disperse to the areas with milder temperatures (i.e., high latitudes/altitudes). Some of these areas are the same climate refuges that have been suggested for the Late Pleistocene. We highlight that 60% of amphibians can become threatened under predicted-future conditions. This work advances the knowledge on climate refuges for amphibian ecology and evolution, supporting complementary tools for conservation strategies.