Abstract Effects of pulsed electric fields (PEF) treatment (0–547 μs and 0–40 kV/cm) on physicochemical properties of soybean protein isolates (SPI) were studied. Solubility, surface free sulfhydryls (SH F) and hydrophobicity of SPI dispersions (20 mg/ml) increased with the increment of the PEF strength and treatment time at constant pulse width 2 μs, pulse frequency 500 pulse per second (pps) and sample flow rate (1 ml/s). When the PEF strength and treatment time were above 30 kV/cm and 288 μs, solubility, surface SH F, and hydrophobicity of SPI decreased due to denaturation and aggregation of SPI by hydrophobic interactions and disulfide bonds. Size-exclusion chromatography and laser light scattering analyses demonstrated further that stronger PEF treatment-induced dissociation, denaturation and reaggregation of SPI. Circular dichroism analysis showed that PEF treatment did not produce significant secondary structure changes of SPI. These results suggested that controlled PEF could be applied to process liquid food including soybean protein ingredient and to modify their structure and function in order to get desired products.