Aims: Cocoa-based agroforestry systems in the Man region of Côte d'Ivoire are essential for balancing agricultural productivity and environmental preservation. This study assessed these systems regarding plant biodiversity conservation and carbon sequestration. Study Design and Methodology: The research was carried out in 21 cocoa plantations, aged between 14 and 32 years, across 60 botanical inventory plots, each measuring 10 by 20 meters. Tree heights and diameters were recorded to estimate Above Ground Biomass (AGB) using the equation AGB = 0.0673 × (ρD²H)0.976, where D is diameter, H is height, and ρ is specific density. Below Ground Biomass (BGB) was calculated as BGB=AGB×0.24, while total biomass (BT) was obtained as BT=AGB+BGB. Carbon stock (C) was derived using C=BT×0.5. Statistical analysis was applied to compare mean carbon stocks across different plantation ages. Results: The plantations, ranging from 8 to 32 years old, showed a diversity of companion species. The diversity of companion species in cocoa agrosystems varies from 4 in 8–10-year-old plantations to 12 in 14- and 15-year-old plantations. Carbon sequestration was age-dependent: younger plantations (5-10 years) sequestered 19.77 ± 2.32 tonnes per hectare, plantations aged 10-15 years stored 133.70 ± 253.50 tonnes, while middle-aged plots (15-20 years) reached 398.76 ± 861.51 tonnes. The oldest plantations (30-35 years) sequestered 137.94 ± 280.31 tonnes. Effective plantation management increased both carbon sequestration and biodiversity. Conclusion: The study highlights the importance of species diversity and continuous management in cocoa-based agroforestry systems. Optimized agroecological practices enhance biodiversity conservation and carbon sequestration, providing practical insights for stakeholders involved in agricultural sustainability, biodiversity conservation, and climate change mitigation. Cocoa agroforestry aligns economic and environmental objectives, offering a sustainable agricultural model.