Hydrodynamic cavitation (HC) is thought weaken the allergenicity of beer gluten proteins. However, the mechanism of action has not been thoroughly studied. In this study, an HC device was used to treat wheat gliadin and two specific celiac-toxic peptides, P1 and P2. FT-IR, MFS, HPLC, and CD were used to monitor the structural characteristics of gliadin and the two peptides. HC reduced the abundance of the coeliac toxic peptides P1 and P2 in solution and the contents of secondary structure β-turns and PPII, which are related to reduced allergen immunoreactivity. This meant that both the primary and secondary structures of P1 and P2 were affected by HC, leading to fewer allergic reactions. This study was focused on the impact of HC on the secondary structures of allergens produced from gluten raw materials, and it has positive implications for reducing product allergenicity.