Assembling between polyphenols and proteins has been freshly spotlighted. We studied the antiglycation and anti-hardening effects of microencapsulated mulberry polyphenols (MMPs) in a high-protein-sugar ball (HPSB) model during storage using multi-dimensional approaches, including UPLC-ESI-MS/MS, SDS-PAGE, MALDI-TOF-MS, FTIR, and a molecular docking study. It was found that MMPs significantly relegated the browning development, AGEs, and/or CML levels of HPSB after 45 d of storage at 45 °C. MMPs also downgraded the protein insolubility, aggregation, oligomerization, and glycoxidation during late-storage. A molecular docking scrutiny proved that cyanidin 3-O-rutinoside and quercetin 3-O-rutinoside interacted with whey proteins subunits via H-bonding and π–π interactions. This binding blocked some glycation residues of whey proteins especially lysyl residues, namely Lys5, 16, 60, 69