Coffee agroecosystems are critical to the success of conservation efforts in Latin America because of their ecological and economic importance. Coffee certification programs may offer one way to protect biodiversity and maintain farmer livelihoods. Established coffee certification programs fall into three distinct, but not mutually exclusive categories: organic, fair trade, and shade. The results of previous studies demonstrate that shade certification can benefit biodiversity, but it remains unclear whether a farmer's participation in any certification program can provide both ecological and economic benefits. To assess the value of coffee certification for conservation efforts in the region, we examined economic and ecological aspects of coffee production for eight coffee cooperatives in Chiapas, Mexico, that were certified organic, certified organic and fair trade, or uncertified. We compared vegetation and ant and bird diversity in coffee farms and forests, and interviewed farmers to determine coffee yield, gross revenue from coffee production, and area in coffee production. Although there are no shade-certified farms in the study region, we used vegetation data to determine whether cooperatives would qualify for shade certification. We found no differences in vegetation characteristics, ant or bird species richness, or fraction of forest fauna in farms based on certification. Farmers with organic and organic and fair-trade certification had more land under cultivation and in some cases higher revenue than uncertified farmers. Coffee production area did not vary among farm types. No cooperative passed shade-coffee certification standards because the plantations lacked vertical stratification, yet vegetation variables for shade certification significantly correlated with ant and bird diversity. Although farmers in the Chiapas highlands with organic and/or fair-trade certification may reap some economic benefits from their certification status, their farms may not protect as much biodiversity as shade-certified farms. Working toward triple certification (organic, fair trade, and shade) at the farm level may enhance biodiversity protection, increase benefits to farmers, and lead to more successful conservation strategies in coffee-growing regions.