The cocoa rehabilitation program in Ghana holds significant value in addressing future climate risks, enhancing food security, and alleviating poverty among farmers, given the country’s heavy reliance on cocoa foreign exchange earnings. Based on this, the study explores farmers’ preferred cocoa farm rehabilitation options with the desired non-market environmental benefits and the associated challenges that must be addressed through a discrete Choice Experiment approach. Respondents ranked eight rehabilitation options developed from a combination of non-market environmental attributes selected from the literature. The results show that pest and disease control was the most influential attribute in the ranking of choice profiles. Higher litter fall, high non-timber forest products, high soil moisture, 75% pests and diseases control, optimum sunlight regulation, and cost of USD 73.4 per acre formed the most preferred rehabilitation option. This study suggests that improving land and tree tenure rights, providing financial assistance, strengthening institutions, and considering farmer-preferred options in policy development could improve farmer interest in cocoa farm rehabilitation, reviving the ecosystem’s health and reversing degradation.