In order to promote cocoa agroforestry by encouraging cocoa farmers to integrate fruit trees inside their cocoa orchards, cocoa certification was initially launched since 2012 in Cameroon. Nowadays, cocoa certification is adopted by a few farmers and makes up only 3% of the national cocoa production. Using the most predominant Fairtrade certification in the South-West region, this study compared certified and non-certified cocoa production via a cost-benefit analysis. The results indicated that, in spite of its supplementary cost expenses (wages to hired workers, agrochemical expenses, transportation charges to cooperatives), certified cocoa production led to higher profit, net present value, internal rate of return, benefit-cost ratio greater than one and shorter pay-back period. For the certified farms, a scenario assuming no certification was analysed and its results testified that the young trees planted during cocoa certification further contributed to raise the farm profit. Overall, the profitability of cocoa agroforest was the highest if the farmer was certified, because of his/her premium earned, training received and adhesion to cooperatives where most group problems were solved. The study therefore recommended farmers to join cooperatives and regularly attend training programmes to learn more friendly environmental practices. In view of this, the government should increase cocoa premium or tie it with payments for full environmental benefits, including rewards for carbon sequestration and biodiversity conservation. The Fairtrade certification bodies should attract reticent farmers to certification by convincing them on the necessity to remove the old fruit trees and replace them with new species, which were more productive to raise their income.