Export banana production in Latin America is pesticide intensive, receiving much negative publicity regarding human health problems and environmental degradation. The Rainforest Alliance (RA) certification scheme was established to certify farms that met a number of social, occupation health and environmental standards set by RA and their certifying body, the Sustainable Agriculture Network (SAN). This study was one of the first, independent studies of the environmental impact of some of the principles set by RA and SAN. The study focuses on insect and bird diversity as an indicator of ecosystem health. Five RA certified farms, six non-RA certified farms, and five organic certified farms were sampled. The data was analyzed with RDA multivariate analyses and Monte Carlo permutation tests. The results showed that RA certified farms had less insect diversity compared to non-RA certified farms and that both farm types had less insect diversity than organic farms. There was little difference between RA and non-RA certified farms with regards bird community composition. Thus, organic farming conserves biodiversity, while alternative environmental labels (e.g. a Rainforest alliance seal) may not have any visible positive effect on in-farm biodiversity. This study points to the need for improvements in SAN certification standards to achieve improved environmental conditions.