Habitat loss and fragmentation, particularly because of agrarian and urban expansions, are threatening biodiversity worldwide. Paraguay is predicted to lose all its primary moist forests by 2028. The most endangered habitat in Paraguay is the Upper Paraná Atlantic Forest (BAAPA), which has been decimated by industrial agriculture in the past 60 years. The hooded capuchin (Sapajus cay) is the best-known Paraguayan primate and the only species mostly restricted to the remaining BAAPA. We used local (defined as people living in Paraguay) knowledge about the known presence of the species in a habitat fragment to assess whether species’ presence was associated with forest cover in fragments by using a binomial general linear model (GLM). Using the results of the GLM, we then assessed how forest cover changed through the hooded capuchin range and its predicted range in Paraguay using Global ForestWatch forest cover prediction for 2000 to 2019. The GLM showed that the presence of hooded capuchins required predominance of forest cover with the monkey being 80% likely to be present for 56% cover and 90% for 70% cover. The capuchin has lost 23% of highly suitable habitat across its whole range and 58% in Paraguay. Suitable habitat for hooded capuchin monkeys is, therefore, decreasing across the full extent of the species. In Paraguay, the remaining habitat is being fragmented and degraded and distance between fragments is increasing. Because the situation in Paraguay is critical, we recommend that the capuchin is classified as Vulnerable by the International Union for the Conservation of Nature and Natural Resources (IUCN) Red List at a national level under criterion B1, b(i), b(ii), and b(iii). Predictions across the species range warrant at least a classification of Near Threatened for the species. These results demonstrate that the conservation situation faced by a primate species can differ greatly depending on local, national, and range wide political and social situations. Therefore, we recommend that national assessments are performed for species that are found in multiple countries in order to gain a true picture of threats a species faces.