Fermented walnut (FW) meal exhibits antifungal activity against Penicillium victoriae (the fungus responsible for prickly pear spoilage), which is mainly attributed to the synergistic effect of antimicrobial peptides and salicylic acid (SA). This study aimed to investigate the synergistic mechanism between YVVPW (YW-5, the peptide with the highest antifungal activity) and SA against the cell membrane of P. victoriae. Treatment enhanced prickly pear’s rot rate, polyphenol concentration, and superoxide dismutase (SOD) activity by 38.11%, 8.11%, and 48.53%, respectively, while reducing the microbial count by 19.17%. Structural analyses revealed β-sheets as YW-5′s predominant structure (41.18%), which increased to 49.0% during SA interaction. Molecular docking demonstrated YW-5′s stronger binding to β-(1,3)-glucan synthase and membrane protein amino acids via hydrogen bonds, hydrophobic forces, and π-π conjugate interactions. Spectroscopic analyses demonstrated SA’s major role in YW-5 synergy at the interface and polar head region of phospholipids, enhancing lipid chain disorder and the leakage of cell components. Malondialdehyde and SOD levels increased nearly two-fold and six-fold when treated with YW-5/SA, and YW-5 showed a more pronounced effect. Scanning electron and transmission electron microscopy confirmed that SA caused greater damage to spore morphology and cell ultrastructure. These findings support this formulation’s functions as an efficient antifungal substance in fruit storage.