Pierce's disease is of major concern for grapevine (Vitis vinifera) production wherever the bacterial pathogenXylella fastidiosaand its vectors are present. Long-term management includes the deployment of resistant grapevines such as those containing thePdR1locus from the wild grapevine speciesVitis arizonica, which do not develop Pierce's disease symptoms upon infection. However, little is understood about how thePdR1locus functions to prevent disease symptom development. Therefore, we assessed the concentrations of plant defense-associated compounds called phenolics in healthy andX.fastidiosa-infectedPdR1-resistant and susceptible grapevine siblings over time. Soluble foliar phenolic levels, especially flavonoids, inX.fastidiosa-infectedPdR1-resistant grapevines were discovered to be significantly lower than those in infected susceptible grapevines. Therefore, it was hypothesized thatPdR1-resistant grapevines, by possessing lowered flavonoid levels, affects biofilm formation and causes reducedX.fastidiosaintra-plant colonization, thus limiting the ability to increase pathogen populations and cause Pierce's disease. These results therefore reveal that differences in plant metabolite levels might be a component of the mechanisms thatPdR1utilizes to prevent Pierce's disease.