This study examined the chemical composition and functional properties of fermented whey beverages produced from organic cow and goat whey, including both acid and sweet variants, enriched with organic sea buckthorn (Hippophae rhamnoides) or rosehip (Rosa canina) juices. In contrast to earlier research primarily addressing physicochemical and technological aspects, the present work offers a comprehensive evaluation of fatty acid composition, mineral and trace element content, antioxidant activity, and total polyphenol levels in these beverage formulations. Both the type of whey and the fruit additive significantly influenced the compositional profile and antioxidant capacity of the beverages. Samples fortified with rosehip demonstrated the highest antioxidant potential, as evidenced by enhanced DPPH radical scavenging activity, elevated FRAP values, and increased total polyphenol content. In comparison, beverages enriched with sea buckthorn juice exhibited higher concentrations of selected minerals, particularly Fe and Ni, while maintaining toxic element levels within permissible limits. The fatty acid profile was predominantly composed of saturated fatty acids, notably C16:0, along with short-chain fatty acids typical of whey. Beverages derived from goat whey contained higher levels of SFA and MUFA than those produced from cow whey, whereas the addition of rosehip contributed to increased proportions of PUFA and omega-3 fatty acids. Collectively, these findings indicate that organic fermented whey beverages enriched with rosehip or sea buckthorn juice may serve as promising functional products with enhanced antioxidant properties and favorable mineral and fatty acid profiles.