In this study, four commercialized indigenous fermented beverages most highly consumed in Russia (kefir and ryazhenka) and South Africa (amasi and mahewu) were analyzed for their potential health-promoting properties and flavor-forming volatile organic compounds (VOC). The analysis of antioxidant capacity demonstrated superiority of dairy-based beverages (kefir, ryazhenka and amasi) over the corn-based mahewu; however, mahewu outperformed dairy-based beverages in terms of its potential antihypertensive effect (i.e., the ability to inhibit angiotensin I converting enzyme). The fatty acid (FA) content of kefir and ryazhenka were more diverse compared to that of amasi, but included a lesser amount of branched chain FA. In terms of calculated FA nutritional indices (e.g., indices of atherogenicity and thrombogenicity), kefir and ryazhenka performed similarly and significantly better than amasi. The agreement between beverages theoretical flavor profiles, which was obtained based on the flavors of individual VOC, and consumers’ flavor perception allow hypothesizing about the contribution of detected VOC to the overall products’ flavor. The obtained data expand current knowledge regarding traditional fermented beverages and their values in terms of national dietary recommendations. Additionally, reported VOC profiles will promote the inclusion of traditional fermented beverages into the rations based on the flavor pairing concept (which is controversial but widely applied).