Indigenous communities manage shaded coffee (Coffea arabica) plantations by applying traditional practices which promote and conserve forest structure and tree diversity while providing a wide variety of environmental services, as well as social and cultural functions. We studied coffee production by a Mixe indigenous community in the Mixe mountains region of Oaxaca, Mexico, to identify the relationship between traditional management of coffee plantations and tree diversity conservation through the analysis of forest structure, richness, composition, and tree uses. A total of 85 tree species were recorded in three classified coffee production areas, the majority of which were natives. Seven species use categories were identified. The results demonstrate variations in coffee plantation structure according to topographic conditions, distance to the community, and management practices. Norms, traditions, and customs of the community guide coffee plantation management. The tree diversity registered in coffee plantations and in uncultivated medium tropical deciduous forest contributes to the maintenance of forest diversity. Thus, traditional coffee management promotes biodiversity conservation. In this particular case, the local community conserves medium tropical deciduous forest within its coffee plantations.