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Transglutaminase (TGase)-mediated crosslinking serves as a promising strategy to mitigate soy antigenicity. β-Conglycinin is recognized as a key allergen among soy proteins. Nonetheless, our understanding of the underlying relationship between immunoreactivity and protein structure remains inadequate. This study aimed to examine the impact of TGase-mediated crosslinking on the immunoreactivity of β-conglycinin in a dual-protein system consisting of soy protein isolate (SPI) and whey protein isolate (WPI) (with SPI-WPI ratios of 10:0, 7:3, 5:5, 3:7 (w/w)). Conformational changes were also examined. Results revealed that β-lactoglobulin and α-lactalbumin in WPI were less susceptible to TGase crosslinking compared to the 7S and 11S subunits in SPI. The conformation of proteins in the dual-protein system after TGase crosslinking were altered, as demonstrated by increased ultraviolet absorption intensity, fluctuant intrinsic fluorescence intensity and surface hydrophobicity, and decreased free sulfhydryl content. As the crosslinking time of TGase increased from 1 h to 18 h, the allergenicity of β-conglycinin gradually decreased in all four SPI-WPI ratios. Notably, the SPI3-WPI7 ratio exhibited the lowest allergenicity of 77.21 ± 1.89% after 18 h of TGase catalyzation. Overall, the dual-protein system proved to be more effective in reducing the allergenicity of β-conglycinin. [Display omitted] • TGase treatment can alter the conformation of soy-cow milk allergenic proteins. • Using TGase can reduce the antigenicity of β-conglycinin, especially in dual-protein system. • SPI3-WPI7 treated by TGase for 18 h had the lowest antigenicity. • TGase crosslinking may be efficient to produce hypoallergenic dual-protein products. [ABSTRACT FROM AUTHOR]