Polyphenolics are a chemically diverse class of plant specialized metabolites with strong antioxidant properties, and their consumption has been associated with improved human health. Metabolomic analysis of these compounds in both plant and mammalian samples has relied predominantly on liquid chromatography coupled to electrospray ionization mass spectrometry (LC-ESI-MS). Due to variable matrix effects across samples during ionization, the accuracy of this approach for quantifying compounds is greatly improved by incorporating stable isotope-labeled standards into the sample prior to analysis. However, commercially available, stable isotope-labeled, polyphenolic standards are both limited and costly. Here we present a protocol for generating stable isotope-labeled polyphenolics based on their deuteration by mild acid-catalyzed, electrophilic aromatic substitution. Importantly, this protocol is effective for generating stable isotope-labeled standards of many biologically relevant polyphenolics, both aglycones and the various conjugated forms alike.