Cocoa beans are the basic ingredient to produce chocolate and its derivatives, including cosmetics, foods, and pharmaceutical products. The quality of cocoa beans is greatly affected by post-harvest handling, especially by microbial activity involved in pre-conditioning after they are harvested, including fermentation, drying, and storage. This review aims to provide various factors that affect each stage of post-harvest cocoa beans, process mechanisms, and various latest technologies that can be used to improve the quality of cocoa beans. Microorganisms could be involved in each post-harvest stage and affect the cocoa beans’ quality. However, fermentation was one of the keys to determining the quality of cocoa beans because fermentation involved various microorganisms, such as yeast, lactic acid bacteria, and acetic acid bacteria, which were interrelated primarily to produce precursor flavor compounds. The drying and storage processes were decisive in maintaining quality, especially in preventing mold growth and other microbial contaminants. Various technologies could improve the quality of cocoa beans during post harvest, especially by adding microbial starters during fermentation. Using several technologies of vacuum drying and a controlled atmosphere during storage could maintain the quality of the cocoa beans. However, many challenges must be faced, especially those related to controlling microbial activity during post-harvest. Therefore, post-harvest technology needs to be continuously developed, especially in controlling microbiological activities to improve the quality of cocoa beans effectively.