Anthropogenic activities are the main reason for the current alarming conservation status of non-human primates (NHP) worldwide, and also lead to habitat-sharing, facilitating human-NHP (interspecific) viral transmission. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for the ongoing COVID-19 pandemic, is well-known for its large genome plasticity and spike proteins (S proteins) highly adaptable to human receptor angiotensin-converting enzyme-2 (ACE2). NHP have been used as models for clinical, diagnostic, and therapeutic studies on SARS-CoV-2 and their correlates. However, the lack of systematic sanitary surveillance in NHP in the Neotropics, as well as the limited capacity to detect infections in their populations, challenge the implementation of consistent epidemiological connections regarding the potential interspecific transmission in the natural environment. Although the natural cross-transmission of SARS-CoV-2 between humans and NHP has not been demonstrated, the global spread of the virus represents a potential threat. Thus, establishing preventive, surveillance, and control measures for viruses of the family Coronaviridae in Neotropical NHP populations is crucial for their conservation.