Fermentation of cocoa beans is the most important process contributing to the flavor in chocolate and other related products. The present study aimed to investigate the fermentation at a laboratory scale of cocoa beans with and without 10% w/w mucilage removal (whole beans). The physicochemical properties and microorganism development were monitored for six days of continuous fermentation (sampling was conducted every 24 hours). The results indicated the effects of partial mucilage removal of cocoa beans before the fermentation, in which the temperature, pH, and mucilage content (with/without mucilage removal) were recorded as 36.5 oC/38.6 oC, 3.44/3.31, and 18.41%/21.84%, respectively at the final day. Besides, the density of microorganisms (yeast-mold, lactic acid bacteria, and acetic acid bacteria) of cocoa beans with partial mucilage removal was higher than whole cocoa beans due to the increased aeration of the beans with mucilage removal, creating favorable conditions for the growth of microorganisms. After the fermentation, several physicochemical properties of the two cocoa bean types were compared, which demonstrated the more favorable quality of the cocoa beans with partial mucilage removal compared to the whole cocoa beans for the fermentation, e.g., lower seed shell content (14.1% vs. 17.8%), lower total acid (1.67% vs. 2.77%), and pH of around 5.0.