<p>Food allergy is a major food safety and public health concern, driven by the increasing consumption of processed foods and the globalization of food supply chains. Industrial processing can profoundly alter the structure, digestibility, and immunoreactivity of food proteins, thereby either attenuating or enhancing their allergenic potential. This review provides a critical and mechanistic overview of how conventional and emerging processing technologies modulate the allergenicity of major food allergens from animal, plant, and microbial sources. Across diverse processing strategies, allergen risk modulation can be systematically interpreted through four fundamental processing-induced “epitope-fate” mechanisms: (i) destruction of epitopes via targeted hydrolysis or enzymatic cleavage, (ii) masking or inactivation of epitopes through aggregation or cross-linking, (iii) exposure or creation of neo-epitopes driven by protein unfolding or chemical modification, and (iv) physical removal of allergenic fractions using separation approaches such as ultrafiltration. The effects of thermal (boiling, frying, roasting), non-thermal (high-pressure processing, irradiation, pulsed light, cold plasma), and bioprocessing methods (enzymatic hydrolysis, fermentation) on allergenicity are comparatively evaluated. Our analysis shows that no single method consistently reduces allergen risk. Thermal treatments vary based on conditions, while high-pressure and enzymatic approaches are more reliable. Robust allergen risk mitigation is most reliably achieved through sequenced, orthogonal processing combinations, which integrate moderate unfolding, targeted proteolysis or fermentation, and physical clearance steps while actively managing trade-offs among efficacy, product quality, industrial feasibility, and the risk of process-induced neo-allergenicity.</p>