Elderberries, sea buckthorn, and sloe berries are fruits of wild-grown bushes, valued in folk medicine for their health-promoting properties but still rarely applied in food. The aim of the present study was to produce probiotic yoghurts with a 10% addition of sweetened purees prepared from elderberries (EPY), sea buckthorn (SBPY), and sloe berries (SPY) and to assess their chemical composition, acidity, content of polyphenols and anthocyanins, ferric reducing antioxidant power (FRAP) and antiradical power (ARP), level of starter microbiota, concentration of acetaldehyde and diacetyl, syneresis, instrumentally measured color and texture parameters, and sensory acceptance. The results were compared to those obtained for plain probiotic yoghurt (PPY) and the changes tracked during 1 month of cold storage at 2 week intervals. The addition of elderberry and sloe berries significantly increased the antioxidant capacity of probiotic yoghurts, probably due to a high content of polyphenols, especially anthocyanins. However, anthocyanins were more stable in the EPY when compared to the SPY. All yoghurt treatments were characterized by good sensory quality and viability of starter microorganisms, including probiotic strains during cold storage. Elderberries promoted the evolution of diacetyl in yoghurts during storage and, together with sloe berries, produced increased syneresis and the greatest changes in color profile compared to PPY.