Protein-polyphenol interactions affect the structure, stability, and functional properties of proteins and polyphenols. Oxidized polyphenols (o-quinones) react rapidly with the sulfhydryl group of cysteine (Cys) residues, inducing covalent bonding between proteins and polyphenols. However, quantitative data on such reactions remain elusive, despite the importance of depicting the significance of such interactions on food structure and function. This work reports the synthesis, purification, and characterization of caffeic acid-cysteine (CA-Cys) and chlorogenic acid-cysteine (CGA-Cys) adducts and their stable isotope analogs, CA-[13C3,15N]Cys and CGA-[13C3,15N]Cys. A sensitive LC-MS/MS isotope dilution method was developed to simultaneously quantify these adducts in foods and beverages. Protein-bound CA-Cys and CGA-Cys were detected in the micro-molar range in milk samples with added CA and CGA, confirming covalent bonding between milk proteins and CA/CGA. These adducts were detected in commercial coffee-containing beverages but not in cocoa-containing drinks. Furthermore, the adducts were found to be partially stable during enzymatic protein hydrolysis.