Advanced glycation end-products (AGEs), which instigate many disorders, are mostly mediated by dicarbonyl rearrangements. We studied the corresponding mechanisms of the anti-glycation effects of two anthocyanins purified from mulberry fruits, namely cyanidin 3-glucoside (C3G) and cyanidin 3-rutinoside (C3R), on glycated β-lactoglobulins (β-Lg). Both mulberry anthocyanins (MAs) inhibited the AGEs-formation in a dose-dependent manner, but the effect of C3R was significantly stronger than that of C3G (p < 0.05). MAs inhibited AGEs-formation by selectively trapping dicarbonyls, especially glyoxal. The UPLC-ESI-Q-TOF-MS results characterized that C3R formed mono- and di-glyoxal adducts, where C3G only created di-glyoxal adducts. Additionally, C3R could directly interact with some of the glycation sites of β-Lg. Overall, GO-trapping and β-Lg-MAs covalent/noncovalent binding are disclosed as the key mechanisms of the anti-AGEs activity of MAs on β-Lg, which could be valorised as effectual AGEs inhibitors in proteins-rich matrices.