Yellow-naped Amazons are IUCN Critically Endangered in the wild. Illegal trapping for trade is the main threat to their survival; habitat loss is ongoing.

The WPT has, since 2007, supported fieldwork; studies led to the species being uplisted to IUCN Critically Endangered.

Beginning in 2021, The World Parrot Trust directly supported the research of a local Costa Rican biologist who aimed to uncover Yellow-naped Amazon population trends in the Santa Rosa region of Costa Rica. Four hundred and twenty hours of nest surveys in February-May and roost counts from June to July found a couple hundred birds at one site, with other new roosts also being discovered.

Despite this, the population in Costa Rica is still declining due to poaching, and agro-landscape changes (converting shade crops to no-shade crops) where roosts once were. Efforts to counter the declines include outreach and contact with landowners interested in having nest boxes put on their properties for the birds. It was determined that even more awareness is needed in local communities. Actions have included active protection against predators, installing nest boxes, and carrying out more nest surveys and roost counts. In 2023, the team installed 40 artificial nests and it is hoped that the Amazons will adopt some of them.