Poultry by-products are promising for the production of protein hydrolysates by enzymatic hydrolysis. The aim of the study is to research the effect of bacterial concentrates on the changes in the amino acid composition and microstructure of poultry by-products during fermentation. Hydrolysis of the gizzards and combs was carried out with a liquid concentrate of bifidobacteria and propionic acid bacteria. As a result of microstructural study of fermented by-products, a decrease in the perception of histological dyes, poor visualization of the cell elements and blurring of the connective tissue matrix were established. During morphometric analyses, we found a reduction in the specific area of connective tissue, the diameter of collagen fibers and the thickness of muscle fibers. A significant effect of the fermentation on the particle size distribution was noted; samples hydrolyzed by microbial enzymes were characterized by a high uniformity of particle sizes and a large number of small particles. Our research revealed an increase in the concentration of free amino acids in the hydrolysates during the fermentation period. The results of biochemical and microscopic analysis confirm the good hydrolysability of hen combs and gizzards under the action of microbial enzymes.