Addressing critical challenges in perishable fruit preservation, including hydrophobic surface treatment, protective layer adhesion on complex cuticles, and synergistic integration of preservation components, here we present an eco-friendly amyloid-like protein coating strategy developed through computer-aided molecular simulation. This system employs phase-transitioned lysozyme as an adhesive layer bonded to fruit epicuticular wax, synergized with sodium alginate and cellulose nanocrystals to form a proteinaceous barrier. Validated across 17 fruit varieties, the coating extends shelf-life by 2-5-fold through microbial inhibition, moisture loss reduction, and rot delay, while maintaining 60–98% nutrient retention, surpassing chemical preservation efficacy without toxicity risks. With edible properties, easy washability, and low cost, the coating demonstrates universal applicability for post-harvest and fresh-cut fruits. Notably, it reduces carbon dioxide emissions by 90% versus refrigeration while achieving 2.5-fold longer shelf-life. These positions the amyloid-like protein coating as a practical and sustainable approach to mitigating global food waste issues.