Although the Black-headed Trogon has a large range, its reliance on rapidly disappearing tracts of tropical dry forest may be a cause of conservation concern. No information is available on current population sizes or population trends, nor on the impact of habitat destruction and deforestation in many parts of its range. Of all the Neotropical trogons, the Black-headed Trogon appears to be most tolerant of degraded forests and human-managed landscapes such as pastures and farmlands; knowledge of its habitat requirements could enable land-owners to better manage their land for conservation purposes.
Some aspects of the life history of this species are well understood, but many fundamental components of reproduction remain undescribed, including courtship, nest-site selection, and copulation. As with many tropical birds, nothing is known about basic demographics such as the age at first breeding, lifespan, and lifetime reproductive success.