Patulin is a mycotoxin mainly produced by Penicillium expansum and commonly contaminates fruits, vegetables, and their derivative products. Patulin degradation by microorganisms or enzymes is currently the most extensively studied method; however, the broader application of these organisms and enzymes is limited by the isolation from products and the requirement of expensive cofactors. In this study, a strain of Papiliotrema flavescens LY3 with excellent patulin degradation capability was isolated. It was further immobilized with magnetic nano-Fe₃O₄ particles by non-covalent electrostatic interactions. P. flavescens LY3 could efficiently convert patulin to E-ascladiol by intracellular enzymes and adsorb patulin with the cell wall. The immobilized P. flavescens LY3 showed no signs of cellular toxicity; moreover, it effectively degraded patulin in apple juice without affecting the juice's main quality indicators. Overall, this study offers a promising biological strategy to mitigate patulin contamination in fruit-derived products.