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This research was carried out to optimize the extraction process of proteins from pomegranate seeds and characterize their in vitro digestibility as well as their thermal and functional properties. For this purpose, the study screened five parameters (liquid/solid ratio, pH, temperature, NaCl concentration, and time) that could potentially influence the extraction process. This screening was conducted using a two‐level Placket–Burman design (PBD). The significant parameters (pH and NaCl concentration) were subsequently optimized using a three‐level face‐centered central composite design (FCCD) to determine the optimum extraction conditions. A maximum protein recovery of 83.8% was obtained at pH 11.0 and NaCl concentration of 0.0 M. Pomegranate seed protein isolate (PSPI) with a protein content of 92.4% (w/w) was obtained through the isoelectric precipitation of pomegranate seed protein extracted under the optimized conditions. An emulsifying activity index of 14.1 m2 g−1 was observed at the isoelectric pH, where the emulsion stability index was at 8.2%. PSPI also showed high water‐ and oil‐holding capacities (3.7 and 4.3 g g−1, respectively). The essential amino acid levels in PSPI (except for valine and isoleucine) exceeded the recommended amounts set by WHO/FAO/UNU for adults, highlighting its high nutritional value. Based on thermal analysis data, denaturation of PSPI could occur at 89.5°C. The in vitro digestibility of PSPI was found to be 74.3%. PSPI shows a potential as a novel ingredient for substituting animal‐based proteins in various food applications. [ABSTRACT FROM AUTHOR]