In the current deforestation context, agroforestry is increasingly considered in the tropical zone for its potential contribution to biodiversity conservation. In Guinée Forestière (Guinea, West Africa), coffee-based species rich agroforests are currently expanding on agricultural land around most villages. To assess the role these agroforests play with respect to biodiversity conservation, we compared their tree structure and diversity with those of a neighbouring natural forest. Eighty plots were sampled using a variable area transect method (60 plots distributed into 3 village agroforests, 20 natural forest plots). The structure of coffee-based agroforests showed obvious signs of farmers’ management: density of mature trees was significantly lower than in natural forest and most juvenile trees were eliminated and replaced by coffee trees. However, tree seedling density was not significantly different than in natural forest. Tree species richness and diversity were also lower than in natural forest but much higher than in any other agricultural or agroforestry land use system. These results are close to those obtained in the coffee-based agroforests of Central America, confirming that coffee-based agroforests retain many forest species that play a key role in the conservation of regional forest tree diversity.