Data on richness and abundance of three taxonomic groups (ants, birds, and trees) were collected in coffee agroecosystems (varying in management style) and nearby forest fragments in Mesoamerica and South America to assess the impact of coffee management intensification on biodiversity. Original data were collected in several regions/countries including Mexico (Veracruz, Chiapas, Soconusco), Guatemala, Peru, Colombia, and Nicaragua. Data were collected in several different projects by the co-owners of the data, but were generally collected between 1993-2006. Bird data come exclusively from 10min 25m radius point count observations. Tree data are species or mophospecies data from coffee or forest plots, and usually include complete enumeration of all trees in the plot. Ant data were collected with variable methods depending on project, but include pitfalls, Winkler traps, tuna baiting, and visual searches. Most projects also included data about the vegetation characteristics in their study sites including canopy cover, tree heights, shade strata, numbers of epiphytes, etc. These project datasets were complied with the extent of conducting a meta-analysis to examine the overall trends in biodiversity decline across coffee systems varying in management intensity.