In coffee-based agroforestry systems under diverse shade tree patterns in Kodagu, Central Western Ghats, India, tree diversity and carbon stock were investigated in both Coffea arabica and Coffea canephora plantations spanning 4106 km2 during 2023-24 and 2024-25. Six distinct shade patterns—native, mixed and exotic species—were assessed under varying management regimes (low, medium and high). Field enumeration recorded tree density, basal area, species richness and structural attributes using nested sampling approaches. Biodiversity indices such as the Shannon-Wiener Index (SWI) and Simpson’s Index (SI) evaluated species diversity and dominance, revealing maximum biodiversity in native and mixed shade systems than in exotic species-dominated systems. The carbon stock distribution was studied across Above-Ground Biomass (AGB), Below-Ground Biomass (BGB) and Soil Organic Carbon (SOC). Arabica plantations recorded higher total biomass (362.43 Mg ha⁻¹) than Robusta (215.50 Mg ha⁻¹), with native and mixed shade systems outperforming exotic systems. SOC contributed over 50 per cent to the total carbon stock, with significant variations across shade patterns and management regimes. Arabica systems showed higher carbon stock (353.06 Mg ha⁻¹) and CO₂ sequestration potential (1294.57 Mg C ha⁻¹) than Robusta systems (272.97 Mg ha⁻¹ and 1000.88 Mg C ha⁻¹, respectively). Native and mixed shade systems exhibited superior SOC accumulation and carbon sequestration potential (1212.02 Mg C ha⁻¹ and 1194.81 Mg C ha⁻¹) compared to exotic systems (1036.34 Mg C ha⁻¹). These findings highlight the ecological importance of native and mixed shade systems in enhancing biodiversity, carbon storage and soil health. The study advocates integrating native tree species for long-term sustainability and resilience in coffee agroforestry systems.