In recent years, carbon dioxide emissions have been potentiated by several anthropogenic processes that culminate in climate change, which in turn directly threatens biodiversity and the resilience of natural ecosystems. Tropical rainforests are among the most impacted biological realms. The Belém endemism center, which is one of the several endemism centers in Amazon, is located in the most affected area within the so-called “Deforestation Arc.” Moreover, this region harbors a high concentration of Amazonian endangered bird species, of which 56% of them are considered to be under the threat of extinction. In this work, we sought to evaluate the current and future impacts of both climate change and deforestation on the distribution of endemic birds in the Belém Area of Endemism (BEA). Thus, we generated species distribution models for the 16 endemic bird species considering the current and two future gas emission scenarios (optimistic and pessimistic). We also evaluated climate change impacts on these birds in three different dispersal contexts. Our results indicate that BAE, the endemic taxa will lose an average of 73% of suitable areas by 2050. At least six of these birds species will have less than 10% or no future suitable habitat in all emission scenarios. One of the main mechanisms used to mitigate the impacts of climate change on these species in the near future is to assess the current system of protected areas. It is necessary to ensure that these areas will continue being effective in conserving these species even under climate change. The “Gurupi Mosaic” and the “Rio-Capim” watershed are areas of great importance because they are considered climate refuges according to our study. Thus, conservation efforts should be directed to the maintenance and preservation of these two large remnants of vegetation in addition to creating ecological corridors between them.