High-power sonication (HPS) is shown to alter protein structure, thus, its functionality, via intermolecular interactions. This study evaluated the effects of HPS on molecular structure of soy proteins in aqueous medium. Free radicals generated during HPS were quantitated using the 5,5-dimethyl-l-pyrrolin N-oxide (DMPO) spin trap method. Electron paramagnetic resonance (EPR) was used to identify them as mostly hydroxyl radicals. The minimum saturation concentration of spin trap solution was determined to be 500 mM of DMPO in water, when exposed to 5 W/cm3 ultrasound power density (PD) for 10 min; subsequently, this concentration was used for quantitating radicals generated in protein samples. Five aqueous soy protein systems, namely, 5% soy protein isolate (SPI), 5% SPI without isoflavonoids (NO-ISO SPI), subunit solutions 1% glycinin (11S) and 1% β conglycinin (7S), and 10% soy flakes (w/v), were sonicated at 2.5 and 5 W/cm3 PDs. Only adducts of hydroxyl radicals (DMPO-OH) were detected in all of these aqueous systems. The highest concentration (3.68 µM) of DMPO-OH adduct was measured in 11S subunit solution at 5 W/cm3, whereas, the lowest (0.67 µM) was in soy flakes solution at 2.5 W/cm3. PD 5 W/cm3 generated higher concentration of radicals in 7S subunit solution, NO-ISO SPI, and soy flakes protein, compared to sonication at PD 2.5 W/cm3. No change in the protein electrophoretic patterns were observed due to HPS. However, some changes due to HPS were observed in the estimated secondary and tertiary structures, and the contents of free sulfhydryl groups and disulfide bonds in proteins.