Soy proteins are globular in nature and are resistant to denaturation with lower intensity thermal treatments like cooking. Likewise, germination can also alter the protein structure through the activity of various enzymes and sonication can disrupt the molecular structure through cavitation and other ultrasound effects, and contribute to some reduction in immunoreactivity (IR) of allergens. This study evaluated the effects of germination and sonication pretreatment in combination with common cooking on lowering the soy allergen IR. Germination was carried out for up to 120 h and ultrasound sonication treatments were given for 20, 40 and 60 min at room temperature. Cooking at 100 oC was carried out for 10 to 60 min. The soy allergen IR was evaluated using a commercial sandwich ELISA kit. The combined action of germination, sonication and cooking helped to reduce the soy allergen IR to single digit mg/L levels from the nearly 400 mg/L initial level in the 5% soy slurry (> 99% reduction). These levels are lower than the reported threshold values of soy allergens in foods. In addition, the germination and ultrasound process was shown to reduce the anti-nutritional properties and enhance the phenolic and radical scavenging activity by over 50%.