Abstract BACKGROUND Walnut protein isolate (WPI), derived as a by‐product of oil extraction, has potential applications in flavor encapsulation and delivery systems. In addition, volatile flavor compounds such as eugenol exhibit poor stability. Eugenol‐loaded nanoparticles were prepared from WPI and soy protein isolate (SPI) using a pH‐cycle technique, aiming to enhance flavor stability and promoting the high‐value utilization of plant proteins. RESULTS Nanoparticles showed high encapsulation efficiency (78.62%) and encapsulation capacity (51.02%), and a particle size of 109 nm, at a concentration of 10 mg mL −1 eugenol. Nanoparticles exhibited remarkable thermal and storage stability, retaining over 70% of eugenol after 30 days of storage at room temperature. Structural characterization and molecular dynamics simulation showed that intermolecular forces, primarily hydrophobic interactions, facilitated the encapsulation of eugenol by WPI and SPI. CONCLUSION These results demonstrate that the pH‐cycle‐induced WPI/SPI nanoparticles provide an effective, green, and energy‐efficient strategy for stabilizing volatile flavor compounds, while highlighting the potential of WPI as a sustainable and cost‐effective material for nanoparticle‐based delivery systems in the food industry. © 2026 Society of Chemical Industry.