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Manufacturing of dark chocolate and other cocoa-based products is a complex multistage process beginning with spontaneous cocoa bean fermentation driven in the postharvest period by different microorganisms derived from the environment. Cocobiota defined as the association of microbial species involved in cocoa bean fermentation may have considerable impact on the medicinal properties of cocoa products via various primary and secondary metabolites, whose presence in dark chocolate and other cocoa-derived products has to be taken into consideration when analyzing medicinal effects of cocoa. Metabolites of acetic acid and lactic acid bacteria, two major cocobiota members, are recently shown to have considerable antifungal and cholesterol-lowering activities and promote the formation of short chain fatty acids and mannitol, an important prebiotic capable of modifying gut microbiota. Penicillium citrinum, a major type of fungi identifiable in fermented cocoa beans, produces a thermostable alkaloid, Penicitrinine A, as well as lovastatin, compounds with antineoplastic and cholesterol-lowering abilities, respectively. Moreover, recent results suggest that bacterial and fungal metabolites produced by cocobiota have a significant anti-infective potential. Therefore, various metabolites produced by cocobiota can mimic some medicinal effects of dark chocolate and other cocoa-derived products previously attributed to cocoa flavonoids and methylxanthines and need to be thoroughly investigated in in vitro and in vivo systems.