It has been documented that certain types of shade coffee plantations have both biodiversity levels similar to natural forest and high concentrations of wintering migratory bird species. These findings have triggered a campaign to promote shade coffee as a means of protecting Neotropical migratory birds. Bird censuses conducted in the El Triunfo Biosphere reserve in southern Mexico have confirmed that shade coffee plantations may have bird diversity levels similar to, or higher than, natural forest. However, coffee and forest differed in species composition. Species with a high sensitivity to disturbance were significantly more diverse and abundant in primary ecosystems. Neotropical migratory birds, granivorous and omnivorous species were more abundant in disturbed habitats. Insectivorous bird species were less abundant only in shaded monoculture. Foraging generalists and species that prefer the upper foraging stratum were more abundant in disturbed habitats, while a decline in low and middle strata foragers was found there. Findings suggests that shade coffee may be beneficial for generalist species (including several migratory species), but poor for forest specialists. Although shade coffee plantations may play an important role in maintaining local biodiversity, and as buffer areas for forest patches, promotion of shade coffee may lead to the transformation of forest into shade coffee, with the consequent loss of forest species.