Since the turn of the century, innovative food processing techniques have quickly risen to the top of the commercial and economic prominence food industry's priority list due to their many benefits over more conventional approaches. Compared to traditional food processing techniques, these innovative procedures retain better the distinctive aspects of food, including its organoleptic and nutritional attributes. Concurrently, there has been a discernible increase in the number of people, particularly infants and young children, who are allergic to certain foods. Although this is widely associated with shifting economic conditions in industrialized and developing countries, the rise of urbanization, the introduction of new eating patterns, and developments in food processing, it still needs to be determined how exactly these factors play a part. Under this circumstance, given the widespread presence of allergens that cause IgE-mediated reactions, it is critical to understand how the structural changes in protein as food is processed to determine whether the specific processing technique (conventional and novel) will be appropriate. This article discusses the impact of processing on protein structure and allergenicity and the implications of current research and methodologies for developing a platform to study future pathways to decrease or eliminate allergenicity in the general population.