Allergens, antinutritional factors, and lipoxygenase (LOX) enzyme present in soymilk limit its consumption as vegan milk. Therefore, the present study focuses on reducing these limiting factors using pulsed electric field (PEF) treatment. In this regard, 20-40kV/cm electric field was applied to soymilk for the effective treatment periods of 450, 1350, and 2250ms. After the treatment, a reduction in pH (6.60±0.10 to 6.47±0.12) and an increase in the conductivity (173.03±0.40 to 177.33±0.72 µS) were observed. Furthermore, FTIR (Fourier Transform Infrared Spectroscopy), UV (Ultra Violet)intrinsic spectra, and CD (Circular Dichroism)spectra (α-helix reduction and β-sheet increase) data indicated mild structural changes in the proteins of soymilk. As a result, PEF treatment reduced the soymilk allergenicity (67.33±20.48%), LOX activity (69.45±9.38%), and trypsin inhibitor activity (75.61±4.04%). Apart from that, the color, viscosity, and volatiles of soymilk also had significant changes due to PEF treatment. The aroma changes in PEF-treated soymilk were highly influenced by two major principal component (PC1 & PC2) groups and they accounted for about 70% of the aroma variations. However, these changes were mild and did not induce any off-flavors and the treatment remained effective against the quality hazards like allergens, antinutritional factors, and LOX enzyme. PRACTICAL APPLICATION: PEF treatment of soymilk reduces the possible allergic reactions in human body at least by 30%. Further, it reduces the antinutritional factor and off-odor inducing compounds. Therefore, the PEF treatment can be used in industries as a pre-treatment to produce allergen and antinutritional compounds free protein isolates from soybeans.