Coffee agroforestry systems (CAFS) have been widely recognized for their potential to support biodiversity, particularly through the retention of indigenous tree species. This study assessed the tree diversity and conservation value of 62 smallholder coffee farms (totaling 39 ha) in the Aberdare Mountains, Central Kenya. Across all farms, 6,642 trees representing 59 species were recorded, with a mean density of 256 trees per hectare and an average of 11.2 species per farm. Indigenous species constituted 63% of the species richness but only 31% of total tree abundance. Farm size positively correlated with species richness but negatively with tree density, indicating trade-offs in land use and biodiversity. Cluster analysis of the 18 most ecologically significant species (based on an importance value index) revealed two distinct farm types: smaller farms (mean 0.4 ha) with higher indigenous tree diversity and density, and larger farms (mean 1 ha) with lower diversity and fewer trees overall. Tree distribution within farms was uneven, with living fences (38%), garden zones (20%), and coffee plots (18%) hosting the majority of individuals. Indigenous trees were more prevalent in fences and gardens. Although 83% of adult trees were planted, only 46% of seedlings were, reflecting farmers’ selective removal of natural regeneration. The farms supported 20% of the region’s native tree species, but only 3.6% of individuals belonged to key forest-dominant species. While these CAFS contribute to structural heterogeneity and landscape-level tree cover, their effectiveness as circa situm conservation reservoirs for indigenous forest trees remains limited.