Coffee is a major world commodity and its production zones overlap with key biodiversity hotspots. The value of the coffee agroforestry systems (CAFS) as reservoirs of biodiversity and buffers for protected areas is well established in Central America and East Africa, but comparatively few studies have been undertaken in India, despite the fact that it produces 4% of the world's coffee. Indian coffee is traditionally grown under shade. Located in the biodiversity hotspot of the Western Ghats, the district of Kodagu produces one third of Indian coffee in complex multi-strata agroforestry systems. The tree cover was traditionally made of thinned-down forest species, providing suitable microclimate to prevent the desiccation of the floral buds, abundant litterfall for nutrient cycling and some degree of control over pests such the white stem borer (Xylotrechus quadripes) and diseases such as leaf rust (Hemileia vastatrix). New management practices including sprinkler irrigation and the conversion from Arabica (Coffea arabica) to Robusta (Coffea canephora) have resulted in important changes in coffee AFS features. Among them were a decrease in canopy cover that enhanced coffee yield, and a gradual replacing of the complex native tree cover by a monospecific cover of Grevillea robusta. While this intensification has increased farmers¿ income, it has also had detrimental effects on the conservation value of the landscape. Through an integrated approach combining large-scale biodiversity assessment and socioeconomic surveys across the landscape, we documented the tree biodiversity associated with coffee AFS of the Kodagu district and explored the socioeconomic drivers behind the species arrangements that compose the canopy cover of these plantations. We identified key management practices and thresholds that could be targeted by public policies for the refining of payment for environmental services and certification schemes aiming at linking livelihoods, provision of ecosy