This study aimed to investigate the effects of hydrophobic and ionic interactions on glycation of native and high-shear treated casein during heating. Casein-epicatechin and casein-calcium complexes were formed and glycated with glucose at different temperatures ranging from 70 to 150 °C in solution and dry states. Furosine, acid derivative of N-ε-fructoselysine (FL), and N-ε-carboxymethyl lysine (CML) were measured as indicators of early and advanced glycation, respectively. CML concentrations of casein-epicatechin and casein-calcium complexes heated in solution were significantly lower as compared to the control (p < 0.05). For instance, 182 ± 9.78 μg/g of CML formed in the control, while CML concentrations were 136 ± 10.7 and 101 ± 7.37 μg/g in casein-epicatechin and casein-calcium complexes, respectively, heated at 150 °C in the solution state. Treatment by high shear microfluidization further decreased the CML formed during heating at 70 °C in dry state. The results suggest that interactions with epicatechin molecule and calcium ion could be a useful strategy to limit advanced glycation of casein under certain conditions.