Food allergens are closely related to their gastrointestinal digestion fate, but the changes in food allergens during digestion and related mechanisms are quite complicated. This review presents in detail digestion models for predicting allergenicity, the fates of food allergens in oral, gastric and duodenal digestion, and the applications of digestomics in mapping IgE-binding epitopes of digestion-resistant peptides. Moreover, this review highlights the structure-activity relationships of food allergens during gastrointestinal digestion. Digestion-labile allergens may share common structural characteristics, such as high flexibility, rendering them easier to be hydrolyzed into small fragments with decreased or eliminated allergenicity. In contrast, the presence of disulfide bonds, tightly wound α-helical structures, or hydrophobic domains in food allergens helps them resist gastrointestinal digestion, stabilizing IgEbinding epitopes, thus maintaining their sensitization. In rare cases, digestion leads to increased allergenicity due to exposure of new epitopes. Finally, the action of the food matrix and processing on the digestion and allergenicity of food allergens as well as the underlying mechanisms was overviewed. The food matrix can directly act on the allergen by forming complexes or new epitopes to affect its gastrointestinal digestibility and thereby alter its allergenicity or indirectly affect the allergenicity by competing for enzymatic cleavage or influencing gastrointestinal pH and microbial flora. Several processing techniques attenuate the allergenicity of food proteins by altering their conformation to improve susceptibility to degradation by digestive enzymes. Given the complexity of food components, the food itself rather than a single allergen should be used to obtain more accurate data for allergenicity assessment.