Shade coffee certification programs have emerged over the past six years to verify that coffee marketed as “shade grown” is actually grown on farms that provide higher quality habitat for biodiversity. In spite of good intentions and an increasing market, little consensus exists on whether current criteria can successfully identify coffee farms of conservation significance. This paper provides the first ecological evaluation and comparison of shade-grown coffee criteria used by major certification programs. Using vegetative data, we evaluated criteria developed by the Rainforest Alliance, the Smithsonian Migratory Bird Center (SMBC), and the Specialty Coffee Association of America across a range of coffee agroecosystems in Chiapas, Mexico, to determine which management practices each program would certify. Fruit-feeding butterflies and forest bird species found in these coffee agroecosystems were compared with nearby forest reserves as indicators of biodiversity and conservation potential. These agroecosystems fall into three categories: rustic, commercial polyculture, and shaded monoculture. The rustic system contained significantly higher fruit-feeding butterfly diversity and an avifauna more similar to that found in forest reserves than the other systems. This was also the only agroecosystem that met the criteria for all certification programs, while the shaded monoculture fell short of all sets of criteria. This suggests that certification programs are succeeding in discriminating between the extremes of shade coffee production. Certification programs differed, however, in their treatment of the intermediate, commercial polyculture systems, reflecting different philosophies for conservation in managed ecosystems. Programs promoted by SMBC use high standards that would exclude all but the most diverse commercial polyculture or rustic systems to certify only those systems that support high levels of biodiversity. The program supported by the Rainforest Alliance only excludes the shaded monoculture while engaging the others in the move toward greater sustainability. The merits of each approach should be put to rigorous debate, and their ability to contribute to biodiversity conservation should be reflected in product marketing. This study suggests that further research can provide a stronger scientific basis and independent verification for the certification of green products that claim to enhance biodiversity conservation in tropical agroecosystems.