Fermentation is an economical method for obtaining protein hydrolysates. The purpose of the scientific research was to perform a comprehensive analysis of the physicochemical, technological, and functional properties of protein hydrolysates obtained by microbial fermentation. The research results showed that hydrolysates fermented with propionic acid bacteria and bifidobacteria have better physicochemical and technological indicators compared to the control sample. Significant increases in water-holding and fat-holding capacities (by 1.8–2.1 times and 1.5–2.5 times, respectively), as well as fat-emulsifying ability (by 12.8–29.8%) in experimental samples were found. Hydrolysates obtained by fermentation effectively inhibit the growth of Escherichia coli and Staphylococcus aureus. The thermal analysis showed a sufficiently high-thermal stability of the obtained protein hydrolysates. In hydrolysates fermented by bacterial culture, the removal of physico-mechanical and osmotically bound moisture occurred at temperatures of 110 °C and 115 °C, respectively, and in whey protein hydrolysate at a temperature of 100 °C. The release of chemically bound moisture was observed at a temperature of 170 °C for fermented hydrolysates and at 155 °C for the control sample. The results proved that fermented protein products are characterized by high functional properties, antioxidant and antimicrobial activity, and can be used as natural food additives and preservatives.