The success of sustainable Theobroma cacao (cocoa) production depends on the physical and chemical properties of the soils on which they are established but these are possibly moderated by the management approach that farmers adopt. We assessed and compared soil physico-chemical properties of young, mature and old organic and conventional cocoa agroforestry systems at two depths (0–15 and 15–30 cm) and evaluated the production of cocoa pods, banana and plantain in the two farm types. Cocoa farms under organic management had 20, 81, 88 and 323% higher stocks of soil organic carbon, P, Mn and Cu, respectively, compared to those under conventional management. Higher soil moisture content, electrical conductivity and pH were found on organic systems than the conventional farms. Annual cocoa pod production per tree was similar in both cocoa systems (Org. 10.1 ± 1.1 vs Con. 10.1 ± 0.6 pods per tree). The annual production of banana and plantain was higher on organic farms (186.3 ± 34.70 kg ha−1 yr−1) than conventional systems (31.6 ± 9.58 kg ha−1 yr−1). We concluded that organic management of cocoa agroforestry systems result in soils with the greater overall quality for cocoa production than conventional management and it increases the yield of co-products. Studies focusing on the impact of organic management on cocoa agroforestry systems at the landscape and regional scales are urgently needed to further deepen our understanding and support policy.