The anthropogenic impacts on the environment, including deforestation and the escalating emissions of greenhouse gases, have significantly contributed to global climate change that can lead to alterations in ecosystems. In this context, protected areas (PAs) are pillars for biodiversity conservation by being able, for example, to maintain the viability of populations of endangered species. On the other hand, the species range shifts do not follow the limits of PAs, jeopardizing the conservation of these species. Furthermore, the effectiveness of PAs is consistently undermined by impacts stemming from land use, hunting activities, and illegal exploitation, both within the designated areas and in their adjacent zones. The objectives of this study are to quantify the impacts of climate change on the distribution of threatened and endemic birds of the Amazon biome, evaluate the effectiveness of PAs in protecting the richness of threatened birds, and analyze the representativeness of species within PAs. We found with our results that climate suitability loss is above 80 for 65% of taxa in the optimistic scenario and above 93% in the pessimistic scenario. The results show that PAs are not effective in protecting the richness of Amazonian birds, just as they are ineffective in protecting most of the taxa studied when analyzed individually Although some taxa are presented as “Protected,” in future scenarios these taxa may suffer major shrinkages in their distributions and consequently present population unviability. The loss of climatically suitable areas and the effectiveness of PAs can directly influence the loss of ecosystem services, fundamental to maintaining the balance of biodiversity. Therefore, our study paves the way for conservation actions aimed at these taxa so that they can mitigate current and future extinctions due to climate change.