Traditional cacao/coffee agroforestry systems (TCCAS) provide environmental services like regulation of water balance, carbon sequestration, soil protection and biodiversity habitat, and supply different products for farmer’s households. However, their low productivity, the lack of incentives and agricultural policies that promote sun cacao/coffee systems as monocrops impose risks to the TCCAS. This study analyzed the knowledge and perception of 90 producers of cacao/coffee about plot management, food, other useful products, and environmental services from different types of TCCAS in Oaxaca and Chiapas, southern Mexico. Three types of semi-structured interviews (~30 min each one) were applied to each producer. Additionally, a tree inventory along a 0.1 ha transect, and field walks into the cacao/coffee plots were made. The findings included a significant harvest from both TCCAS, which may contribute to the diversity of diet and food security of farmers. Fiftytree species and 38 wild animal species were reported. We also found ≥ 50% vegetation cover, which protects soil and helps water infiltration. Thus, TCCAS may be considered as sustainable production systems. Thus, market, food sustainability movements and biodiversity conservation incentives need to be channelledto protect this form of production of two food products massively consumed around the world.