This paper aimed to study the biodegradation of collagen-containing waste (pork skin) induced by collagenase and Neutrase 1.5 MG enzymes and compare the amino acid, peptide, and carbohydrate composition of hydrolysis products. It was found that the degree of biodegradation of collagen-containing raw materials (pork skin) reached 78% when using an enzyme preparation (collagenase with a concentration of 250 U/g of the substrate) at pH 7.0, 40 °C, and a 360 min process duration. It was shown that the content of peptides with a molecular weight of 6.5–14.0 kDa in the hydrolysis products (collagenase) of collagen-containing wastes was 13.4 ± 0.40%, while in the products of hydrolysis (Neutrase 1.5 MG) it was 12.8 ± 0.38%. The study found that the hydrolysis products (Neutrase 1.5 MG) of collagen-containing raw materials contain fewer hexoses, free hexosamines, and hyaluronic acid than the hydrolysis products (collagenase) of collagen-containing raw materials. The content of chondroitin sulfates is practically the same in all samples of hydrolysis products. Proteases with collagenolytic activity are widely used in industry. Recently, they have increasingly been used in pharmaceutical, food, and other industries. Collagenases are promising enzymes for the production of chondroprotectors used for the treatment of osteoarthritis.