Soymilk, valued as a protein-rich animal milk alternative, faces consumption challenges due to allergenicity, antinutrients, and undesirable odors from lipoxygenase (LOX) activity. Therefore, soymilk samples were subjected to plasma bubbling (PB) at 100 and 200 V voltage levels for 5, 15, and 25 min to address these issues. Post-treatment, significant changes were observed in Fourier-transform infrared amide regions (I-1631 cm −1 , II-1537 cm −1 , and III-1238 cm −1 ), circular dichroism spectra (less α−helix and turns; more β−sheets), intrinsic fluorescence (blue shift at 343 nm), and sodium dodecyl sulfate-polyacrylamide gel electrophoresis protein profiles. As a result, the soymilk allergenicity, LOX activity, and trypsin inhibitor activity (TIA) were reduced to 38.99 ± 17.7, 79.26 ± 3.74, and 91.71 ± 10.64%, respectively. Meanwhile, mild changes were observed in the pH, conductivity, whiteness values, viscosity, and protein content of treated soymilk. However, E-nose analysis identified pungent and grassy flavors in treated samples due to oxidation. Therefore, PB is highly effective against allergenicity compared to LOX and trypsin inhibitor activities.