The role of agricultural systems in conservation has been subject to heated debate in recent years. Some experts argue that agricultural areas threaten biodiversity and their expansion should be deterred. Others signal that some agricultural systems conserve biodiversity and provide ecosystem services. We surveyed 137 agronomists, ecologists and environmentalists working in Mesoamerica to understand their ideas regarding social and biological attributes of agroecosystems and their relevance to conservation. We quantify perceptions of the advantages and disadvantages of distinct Mesoamerican agricultural systems with respect to conservation. Respondants generally agree that monocrops (soy beans, rice, pineapples, bananas, tree crops) and pastures degrade the environment, while agroforestry systems (shade coffee, silvopastural systems) preserve biodiversity and provide ecosystems services. Interestingly, the milpa (traditional polycrop of corn, beans, and squash) is also considered to preserve biodiversity and provide ecosystems services, despite its treatment in the conservation literature as a major cause of deforestation in Mesoamerica. For the professionals who answered the survey, ecological attributes are as important as socioeconomic attributes to evaluation of system performance. A system’s capacity to meet farmers’ food, clothing and housing needs is as important as its associated biodiversity or the ecosystem services that it provides. Neither profession nor country where field work is performed had significant relationships with survey responses. Professionals who live in the USA assign slightly more weight to ecological attributes of production systems than do Mesoamericans. Our results may help direct public policy and identify knowledge gaps to be filled by further research.