The current study was conducted to investigate the recovery of native potato protein from potato fruit water (PFW) by expanded bed adsorption (EBA) chromatography. The eluted proteins were concentrated by ultrafiltration and spray-dried into powder. The SDS-PAGE showed that the recovered proteins were potato protease inhibitors (PPIs). The trypsin and chymotrypsin inhibitor activities of the recovered PPIs were 377.93 ± 8.22 and 12.90 ± 0.03 mg g⁻¹ protein, respectively. The recovery yield of protease inhibitors was 74.88%. The glycoalkaloid assay showed that the recovered PPIs contained 30.31 ± 0.15 μg g⁻¹ of α-chaconine and 92.77 ± 0.52 μg g⁻¹ of α-solanine, and these values were much lower than those in potato protein concentrate (PPC) obtained by traditional thermal coagulation. The most abundant amino acid in the PPIs was serine. The results indicated that the EBA can be used to effectively recover native potato protein from PFW.