Soybean, the world’s primary provider of protein and oil, is widely used in foodstuffs which might pose a serious threat to allergic consumers due to the presence of some allergenic proteins. Enzyme-linked immunosorbent assay (ELISA) is the preferred method for the determination of allergen contamination in foodstuffs. Due to food processing, the antibody–antigen interaction in these routinely used methods are disrupted, therefore leading to erroneous results. A comparison between an ELISA using antibodies against modified soybean proteins and against the Kunitz trypsin inhibitor (KTI) is described. Limits of detection and quantification of 115.6 ng soybean protein/mL and 346.8 ng/mL were obtained for soybean-ELISA and 117.3 ng KTI/mL and 351.9 ng/mL for KTI-ELISA, respectively. Minimal cross-reactivity with other legumes and food ingredients were obtained. The applicability of these ELISAs was evaluated to detect the presence of soybean proteins in cookies. Both matrix interferences and the baking process affected analytical recovery. However, the recoveries were found to be much higher using the soybean-ELISA. The low recovery obtained using the KTI-ELISA might be due to the inability of the antibodies used to recognize the modified proteins. These results indicate that using antibodies developed towards allergens modified through food processing simulating reactions is a better approach to be used in food allergen detection.