In the actual context of food safety and circular economy, the separation of the α137-141 antimicrobial peptide (TSKYR, 653 Da) coming from the hydrolysis of bovine hemoglobin, a non-valorized slaughterhouse by-product, and its reuse as a preservative agent for food products during storage would be of major interest. However, depending on the degree of hydrolysis (DH) of the bovine hemoglobin, the TSKYR peptide environment into the hydrolysate will be different and would impact its recovery yield by electrodialysis with ultrafiltration membranes (EDUF), a hybrid and eco-friendly technology. In this context, five DHs (3, 5, 10, 13 and 18%) were investigated to study the influence of the peptide populations on the α137-141 selective separation by EDUF. It appeared from these results that the most appropriate DH was of 5% since a lower population of peptides between 500 and 1000 Da was present and the subunits of hemoglobin were already digested. Hence, an enrichment factor of about 13 folds for the α137-141 was obtained in comparison with the initial hydrolysate. At our knowledge, it was the first time that the effect of the hydrolysis degree of a protein is demonstrated to impact preferentially the separation of a specific peptide by EDUF.