Fractionation of β-lactoglubulin (β-lg) and α-lactalbumin (α-la) using conventional separation technologies remains challenging mainly due to similar molecular weight. Herein, casein (CN) was used as ligand protein to specifically aggregate β-lg under high hydrostatic pressure (HHP) in order to separate α-la after acidification to pH 4.6. Specifically, we studied the effect of different concentration of CN on α-la purity and recovery. Model solutions of α-la, β-lg and CN (from 0 to 5 mg/mL) were pressurized (600 MPa–5 min). After acidification and centrifugation of pressure-treated solutions, purity of α-la was increased up to 78% with a recovery of 88% for solution without CN. In contrast with our initial hypothesis, the presence of CN decreased β-lg pressure-induced aggregation and co-precipitation upon acidification and significantly reduced purity (∼71%). Therefore, our results suggest a chaperone-like activity of CN on β-lg pressure-induced aggregation which needs further investigation.