Across Amazonia, apart from pre-Colombian agricultural practices and sparse modern urban areas, native habitats remained mostly intact up until 1970’s. In the last 50 years, large infrastructure projects such as highways and river dams were the venue for increasing deforestation and habitat conversion rates in the countries comprising the Amazon region. The fast pace of environmental change in Amazonia affects animal and plant species. Although the IUCN Red List already provides detailed threat assessments for most bird species, new studies re-evaluating the taxonomic status of Neotropical birds show that many lineages currently treated as subspecies of Amazonian birds should be recognized as full species. IUCN threat assessments do not follow closely the constant changes in taxonomy, and this may be signalling a false scenario for the conservation status of Amazonian birds. To assess the IUCN conservation status of all Amazonian bird taxa (species and subspecies) based on their range size (IUCN criterium B), we built a point locality database with c.620,000 records where we identified each record at the subspecies level for 3,320 taxa. We built custom extent of occurrence range maps for all the 3,320 taxa based on their point localities and on expert scientific knowledge. We used the point locality records from each taxon to generate environmental niche models, projecting suitable habitats within their extent of occurrence (EOO) maps in present and future climate scenarios, also incorporating current and future projected deforestation information. Our results show that at least 27% (901 of 3,320) of Amazonian bird taxa should be classified within one of IUCN’s threat statuses, and that within future climatic and deforestation conditions, up to 47% (1,559 of 3,320) of Amazonian bird taxa should be considered threatened. Among these, 60% (939 of 1,559) are either from montane evergreen forests from the eastern Andean slopes, or from the lowland evergreen forest (terra-firme) of the southeast portion of Amazonia. Our study reveals the importance of evaluating threat status of Amazonian birds at the infraspecific level and calls for immediate conservation effort to protect animal communities which are still poorly understood in the most bird diverse region of our planet.