The ongoing introduction of the exotic Grevillea robusta tree species into agroforestry systems (AFS) of the Indian Western Ghats could become a threat to both climate change mitigation and tree diversity conservation. Here, we quantified carbon (C) storage and shade tree diversity in native forests and coffee AFS under contrasted management (native versus exotic shade trees, Robusta versus Arabica systems) at 67 plots along a 3500 mm precipitation gradient in the Cauvery watershed, India. Despite a substantial reduction of shade tree cover in native AFS compared to forest (from 90% to 32% in the high precipitation area), native AFS and forests displayed high and comparable C stocks (max. 228 MgC ha−1 and 234 MgC ha-1, respectively) and tree diversity (max. 44 and 45 species, respectively). Both variables were negatively impacted by the introduction of G. robusta, especially in Robusta coffee systems (max. 158 MgC ha−1, 12 species). The current trend toward the introduction of G. robusta in coffee AFS of the study area (exotic agroforestry) negatively affects C storage and tree diversity, especially in Robusta coffee systems. Policy makers should take advantage of the carbon-tree diversity positive correlation found in the agroforestry landscape of the Western Ghats of India to promote conservation and climate change mitigation.