The aroma, taste, shine, snap, smoothness, "melt-in-your-mouth" sensation, and texture are all qualities that define chocolate, and all depend on how the cocoa and the chocolate itself are processed. Postharvest handling of the cocoa (fermentation, drying, cleaning, storage, and transport) and its transformation into chocolate (roasting, grinding, conching, tempering, molding, and the addition of core and other ingredients), as well as the packaging, storage, transport, and refrigeration of the finished product all have an important influence on the characteristics of chocolate. The aim of this review was to identify and study the key factors, including microbiological aspects that affect the quality of chocolate, from harvesting the beans right up to the manufacture of the finished products.