Abstract Food processing and interactions involved in different food components affect the bioavailability and immunoreactivity of allergens. However, the impact of food processing and food matrices on protein digestibility and immunoreactivity of allergens are poorly understood. Digestibility of baked wheat-based matrix was assessed using an in vitro digestion system which includes a model chew, followed by simulated gastric and duodenal digestion system. Protein digestion was monitored by SDS-PAGE, and immunoreactivity was specifically analyzed by immunoblotting using monoclonal antibody. Peanut and wheat allergens were rapidly digested after exposure to pepsin. The wheat allergens are degraded into low molecular weight polypeptide. The peanut allergens, like Ara h1 and Ara h3 in soluble protein were almost disappeared, and Ara h2/6 was resistant to gastro-intestinal digestion. The result of ELISA showed the decreased of allergenicity of allergens after digestion. The digestive stability was not affected by baked wheat-based matrix, and the immunoreactivity was reduced by digestion.