This study demonstrated multiple sensory profiles of fermented cocoa beans in Indonesia. The concentrations of the chemical compounds are attributed to the flavor variations. Genetics, geographical, climatic, and postharvest processing were among the influencing factors. Of these, modification of postharvest processing techniques is the most feasible means to modulate the flavor of cocoa beans. Finally, the diversity in the sensory characteristics allows the exploration of new sources of fine-flavor cocoa beans from Indonesia.Post-harvest handling of cocoa beans needs attention, starting from picking the pods, sorting, ripening the pods, fermenting, drying, and storing. The activity of microorganisms in each post-harvest stage affects the quality of cocoa beans. Fermentation is one of the important stages involving microorganisms such as acetic acid bacteria, lactic acid bacteria, and yeast which play a major role in producing precursor flavor compounds in cocoa beans. However, harmful microbes such as pathogenic bacteria and fungi can contaminate and reduce the quality of cocoa beans. Mold contamination causes weathering, reduced nutrition, and the presence of mycotoxins. Improvement of cocoa bean quality can be carried out by adding a starter culture in fermentation. The addition of these cultures can increase the fermentation rate and improve the biochemical process in cocoa beans. Proper drying processes and controlled storage can maintain the fermented cocoa beans'quality. However, many difficulties and challenges remain, especially those related to controlling microbial activity during post-harvest. Post-harvest technology needs to be continuously developed, especially in controlling microbiological activities to improve the quality of cocoa beans.