Cropping systems have influence on the conservation of soil organic matter. Soil samples were taken from a long term experiment that was designed to study the impact of shade and cocoa plant densities on cocoa yields. The impact of the treatments on soil organic carbon sequestration rates and the gains or losses of soil organic carbon under the treatments with reference to adjacent undisturbed bush were assessed. The experiment was sited at the Bunso substation of the Cocoa Research Institute of Ghana on Rhodi-lixic ferralsol with annual precipitation of about 1500 mm. The shade was provided by forest trees of 18 trees ha-1 and no shade, while the cocoa densities were 1111, 1428 and 1667 trees ha-1. Shade effects on organic carbon pools within the top soil (0-30 cm) under cocoa were not significant (p=0.05). Cocoa plant densities per unit area influenced the soil organic carbon pools. The soil organic carbon pools were significantly lower (p=0.05) in the closely planted farms than in the widely spaced farms. There were no soil organic carbon sequestration in the highest cocoa plant density of 1667 trees ha-1 but 250 and 190 kg soil organic carbon ha-1 yr-1 in the top soil (0-15 cm) were sequestered in the soils under cocoa with density of 1111 trees ha-1 for shaded and unshaded farms respectively. Irrespective of the shade conditions, the net gains of carbon in the soils were higher in farms with lower cocoa plant density. The results suggest that cocoa planted at low plant density under shade stores more carbon per unit area of soil than an equivalent area of cocoa planted at high density without shade. It is concluded that cocoa farming could be an effective means to mitigate carbon dioxide emissions in cocoa growing countries.