The enzymatic hydrolysis of proteins is hindered by product inhibition during batch reactor operation. Thus, withdrawing reaction products has been proposed to increase the reaction efficiency. The sequential batch strategy was evaluated for the hydrolysis of salmon frame proteins by subtilisin to improve the efficiency of the process. After one hydrolysis batch the soluble phase was withdrawn, and the remaining solids were further hydrolyzed in the absence of the inhibition products. The operation of two sequential batches were compared to a one-stage batch operated for 2 h with 13 AU subtilisin per kg of salmon frame at 55 °C. The one-stage batch yielded 27% nitrogen recovery after 2 h of reaction. The sequential batch operation yielded 22% and 24% nitrogen recovery in the first and second batch, respectively, resulting in a total of 46%. The second batch yielded 21% when operated without protease addition, resulting in a total yield of 42%. Different distributions of the operating time and protease dose between the first and second batch were tested. The sequential batch strategy resulted in a higher productivity and lower operating costs for the enzymatic hydrolysis of salmon frame proteins, representing significant progress in byproducts valorization and circular economy.