The development of rootstocks that are less sensitive to abiotic and biotic stresses can help mitigate the negative effects of climate change on crop productivity, soil health, and water use. Though, the phenomenon of graft incompatibility is a significant limitation to the spread of new rootstock genotypes. Numerous studies have focused on this issue, highlighting the role of certain phenolic molecules as predictive markers of incompatibility. Given the lack of specific research on table grape, , this study proposes a protocol for the extraction of polyphenols from its woody tissues, which is a fundamental prerequisite for further analysis on secondary metabolites involved in graft incompatibility. The proposed eco-friendly method coupled a traditional maceration using solvent with a green technique utilizing an ultrasound-assisted extractor. The following parameters were compared: (1) sample weight (0.1 g, 0.5 g, and 1 g), (2) time of ultrasound-assisted extraction (10 min, 20 min, and 30 min), and (3) solvent volume for maceration (10 mL, 15 mL, and 20 mL). Four phenol classes were considered based on previous works on <i>Vitis</i> spp.: cinnamic acids, flavonols, benzoic acids, and catechins. The characterization of polyphenolic biomarkers was carried out via HPLC. 1 g of plant material, 30 minutes of sonification, and 20 mL of organic solvent was the combination of factors that resulted in the most efficient fingerprint, both quantitatively (267.68 ± 3.91 mg/100 g fresh weight [FW]) and qualitatively, with the four classes analyzed significantly represented. This is the first work to come up with an extraction protocol for phenol compounds in table grape woody tissue based on both ecological and routine techniques.