Cocoa-based agroforests play an important role in farmer livelihood and the global environment; however, despite these facts, their low yields and tree aging put at risk their fate. This project investigated the carbon storage potential, productivity, and economics of different agroforestry arrangements of cocoa (Theobroma cacao) with Melina (Gmelina arborea) trees, in the southwest of Colombia. We established the experiment under a Randomized Complete Blocks design with seven treatments and three repetitions. Different allometric models were tested. Allometric models were made for G. arborea trees with dbh, ranging between 30.24 and 50.11 cm. The total carbon accumulation fluctuated between 49.2 (Treatment 4) and 88.5 t ha−1 (Treatment 2), soil organic matter (SOM) ranged between 9 and 17%, bulk density decreased from 0.83 to 0.77 g cm−3. Cocoa yield ranged between 311 kg ha−1 year−1 (Treatment 7, traditional farm) and 922 kg ha−1 year−1 (Treatment 6). Treatment 6 showed the best performance with a net present value (NPV) of COP 1,446,467 (US $337.6), an internal rate of return (IRR) of 42%, and a cost-benefit ratio (B/C) of 1.67%. The benefits of AFS were also evidenced in some of the physical and chemical soil properties. Despite local marginality, these cocoa agroforest arrangements are a viable alternative to improve the traditional (local) cocoa systems because cacao agroforest arrangements increased cacao yield and carbon storage becoming a suitable alternative to improve traditional systems.