Coffee agroforestry is considered a promising alternative to conventional agriculture that may conserve biodiversity while supporting local livelihoods. This study analyzed the capacity of coffee agroforestry to conserve the tree species diversity and community composition found in forests in La Sepultura Biosphere Reserve in Chiapas, Mexico. To meet this goal, we compared coffee agroforests to forest in terms of floristic richness estimated by tree species richness, Shannon and Simpson Reciprocal diversity indices, and accumulation curves; vegetative structure characterized by basal area, canopy closure, shade tree density, and coffee shrub density; tree community composition described by non-metric multidimensional scaling ordination and by traits of succession (pioneer, intermediate, and late successional); and the presence and abundance of tree species of conservation concern. We found that, although at the landscape level the ensemble of coffee agroforests may conserve comparable species richness to forests, the species ensemble that is being conserved in coffee agroforests is different from that found in forests. Coffee agroforests were dominated by Inga spp., harbored lower tree species diversity at the plot level, a higher proportion of pioneer trees, lower proportion of trees of conservation concern, and were different in terms of community composition compared to forests. Due to these significant differences in tree diversity and community composition between coffee agroforests and forests, we suggested that conservation practitioners and policy makers seeking to promote coffee agroforestry as a conservation strategy should be mindful of whether coffee expansion is occurring in forests or land previously used for agriculture. Whenever appropriate, strategies and policies should impulse the conversion of crop monoculture and pastureland into coffee agroforests, thereby sparing forests and reforesting tree-less agricultural land. Conservation strategies should also discourage the replacement of diverse forest canopies by Inga-dominated coffee agroforests.