Effect of low doses of gamma irradiation (0.25, 0.5 and 1.0 kGy) on protein oxidation, profile, solubility, ROS scavenging and in vivo bioavailability of minerals in black (BS1) and yellow (BRAGG) soybean varieties were investigated. Increased oxidation, altered protein profile with decreased solubility was observed higher in BRAGG compared with BS1. The most significant ROS scavenging effect, antioxidant activity, least phytate content and improved bioavailability was found at 0.5 kGy in BS1 than BRAGG due to anthocyanins, and phenolics. Still 1.0 kGy is considered as toxicologically and microbiologically safe but it causes biochemical alterations and thus 0.5 kGy can be the optimum dose with enriched nutraceutical properties.