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The rapidly developing food industry necessitates the efficient use of raw materials, which can be achieved through the production of functional ingredients with high nutritional value. Secondary fish raw materials generated during the filleting of Atlantic cod (Gadus morhua), including vertebral bones with residual muscle tissue, skin, tails, and fins, represent a promising source of both biologically active compounds and highly digestible protein substances. The aim of this study was to evaluate the properties of protein hydrolysates obtained from secondary Atlantic cod raw materials by conventional enzymatic hydrolysis and combined enzymatic-ultrasonic treatment. The best results were achieved at a power of 320 W and a treatment duration of 3.5 min prior to the addition of the enzyme preparation (Protozyme C). The application of ultrasound enhanced the degree of hydrolysis by 4–5% while simultaneously reducing the amount of enzyme used. Electrophoretic analysis demonstrated a predominance of smaller peptides in the 10–15 kDa range compared to the control sample (43–95 kDa). Infrared spectroscopy confirmed structural changes in the samples under study, manifested in an increase in the number of terminal groups and partial disaggregation of the peptide mixture. Particle size distribution analysis revealed a more uniform distribution and a decrease in the median particle size in samples with ultrasonic pretreatment. The safety and antioxidant activity assessment did not show any toxic effects, but manifested a significant increase in antioxidant indicators (2.5–3.2 times) compared to the control sample. The results obtained show the enzymatic-ultrasonic treatment to be promising for the integrated processing of fish raw materials and the production of functional food ingredients with improved properties. Full article