Owing to the combined characteristics of low allergens and lipids, as well as high versatility and abundance, eco-friendly pulse-based protein has served as a critical contender to supplement animal protein. The inferior solubility and off-flavor, however, place a practical restriction on its application. Glycation via Maillard-driven reaction is a potential green chemistry to modulate protein structure and functions. The various types of protein, saccharides with different molecular mass and structural characteristics, and two reaction systems (dry and wet heating) were applied to synthesize protein-saccharides conjugates. The aims were to investigate (i) the effect of glycation on functionalities and flavor of pulse-based protein using above-mentioned elements, and (ii) mechanisms by which glycation affects the protein architectures and modulates its functionalities. SDS-PAGE, SEM and FTIR-ATR were applied to confirm the successful development of protein-saccharide conjugates. The extent of glycation was time-dependent, and 11S and 7S globulin were mainly responsible for conjugation with gum Arabic (GA) under dry heating conditions (60°C, 79% relative humidity, pH 7.0). Glycation significantly improved protein solubility at neutral pH, whereas such effect varied depending on the protein source and reaction time. The stability of emulsion against environment stress and lipid oxidation gained a significant improvement, which was attributed to electrostatic interactions and stronger steric hindrance of protein-GA conjugates. HS-SPME-GC-MS analysis indicated glycation is a promising approach to mitigate the beany flavor, presumably because of the alterations in protein structure resulting in release of unpleasant odorants. The solubility of pea protein was sufficiently improved after glycation, while its thermal stability was remarkably lowered under wet heating conditions (80°C, pH 10.0). The proposed principle involved glycation via Maillard-driven chemistry enhanced the surface hydrophilicity of protein and unfolded its spatial architectures.