Shade coffee agroforestry systems have the potential to support biodiversity. Sustainable certification of coffee has been promoted as a means to provide incentives to maintain these systems, but as yet there is little evidence if this is effective. We analyzed tree diversity on smallholder organic and conventional farms in buffer zones of three conservation areas in Costa Rica, Guatemala and Nicaragua (the later included some large-scale conventional and Rainforest Alliance certified farms). Organic farms had greater farm level tree species richness and Shannon diversity compared to conventional farms; estimated native tree species richness across the landscape was probably greater on organic farms than conventional in Nicaragua (48 versus 28 species respectively) and possibly in Guatemala (23 versus 15 species respectively). Organic farms had higher shade levels and more tree strata than conventional farms. In Guatemala and Nicaragua tree species composition was not closely related to whether farms were organic or conventional, although within composition clusters, organic farms tended to have greater diversity. In contrast, organic and conventional farms in Costa Rica mostly belonged to different tree species clusters. In Nicaragua most large-scale farms, and all Rainforest certified farms, formed a distinct species composition cluster with presence of old-growth forest species and within which Rainforest farms had greater diversity. Tree species composition of the shade seems to be mainly due to management history; but certification effectively differentiates those farms with greater tree diversity. Longer-term monitoring is required to determine whether certification can be an incentive to conserve or expand biodiverse coffee agroforestry systems within the buffer zones around conservation areas.