Commercial soy-based foodstuffs, including beverages ( n = 15), cow's milk supplemented with soy isoflavones ( n = 1), snacks ( n = 1), and biscuits ( n = 2), were analyzed to find any link between alterations in protein quality, safety (antigenicity), functionality (antioxidant activity), and food processing. Protein content was analyzed by the Kjeldhal method and available lysine by OPA assay. Chromatographic (RP-HPLC) and electrophoretic (SDS-PAGE) protein profiles were obtained to monitor modifications in the structure of soy allergens. The antigenicity was estimated by immunoblotting against soy total antibodies. Total phenol content was measured by Folin-Ciocalteu, while peroxyl radical scavenging activity of the sample was determined by ORAC FL assay. Protein content did not differ of those declared by the producers. Lysine availability was higher in liquid soy beverages compared to that in other soy foodstuffs studied here. 7S and 11S soy allergens were detected by RP-HPLC and SDS-PAGE, respectively. Both data indicated changes in soy protein patterns due to processing of instant powdered soymilk, soy snacks, and biscuits. Immunoblotting assay showed modifications in the antigenic response of these foodstuffs based on soy, suggesting that their processing had altered the structure of soy allergens. RP-HPLC, SDS-PAGE, and immunoblotting resulted in adequate analytical approaches for detecting changes in protein structure due to processing and adulteration. Protein quality, antigenicity, and antioxidant activity of soy products can be affected as a function of the intensity of the thermal processing.