Specialty coffee (SC) production enables farmers to earn premium prices for high-quality coffee. In Bolivia, some coffee-based agroforestry systems (CAFS) produce SC. However, while many Bolivian families’ livelihoods depend on coffee, studies on SC-producing CAFS remain scarce. Yet, research on tree diversity, CAFS management and the factors affecting tree diversity can offer novel insights on agroforestry. We sampled 24 farms in three villages located in the Caranavi municipality. We analyzed farms main characteristics, biophysical variables, shade tree diversity, tree uses, management practices and farmers’ socioeconomic background. Additionally, we surveyed 50 coffee farmers to collect information about preferences for tree species and tree characteristics. Then, we investigated if farmers’ socioeconomic and farm biophysical variables affect CAFS tree species richness and tree density using generalized linear models (GLM). Our results showed that studied farms are small and certified properties (average: 2.6 hectares) managed by families; we observed that CAFS provide farmers with useful products besides SC. 85 tree species, primarily serving as shade providers for coffee, were identified. These species also yield valuable resources like: fruits, timber, lumber, and medicinal products. Accordingly, surveyed farmers exhibit preference for tree species offering useful and marketable products, with tree characteristics selected based on their advantages for coffee and farmers. GLM revealed that socioeconomic and biophysical variables affect species richness and density. Additional research is needed to evaluate the relationship between biodiversity and the social-economic sustainably of Bolivian CAFS. Likewise, is necessary to enhance farmers’ ability to manage their CAFS for biodiversity conservation and household wellbeing.