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The objective of this work was to optimize the ultrasound-assisted extraction process of bioactive compounds from byproducts of V. vinifera and C. sinensis using the Taguchi methodology. Moreover, the flavonoid content and the subsequent evaluation of the antioxidant potential through three different assays (ABTS∙+ radical inhibition, ferric-reducing power (FRAP), and OH• radical inhibition) were determined. Furthermore, the potential of these metabolites to inhibit the α-amylase enzyme and their protective effect to inhibit the hemolysis due to oxidative processes was assessed. In addition, functional group analysis was performed using Fourier transform infrared spectroscopy. The Taguchi L9 statistical model enabled the increase in bioactive compound yields by evaluating factors such as particle size, temperature, time, and solvent concentration. The samples were found to contain flavonoid-type compounds, which translated into their ability to inhibit free radicals (ABTS∙+ and OH•) and act as reducing agents (FRAP). They exhibited inhibitory effects on the α-amylase enzyme involved in the assimilation of starch and its derivatives, along with providing over 50% protection to erythrocytes in the presence of free radicals generated by AAPH. Furthermore, FTIR analysis facilitated the identification of characteristic functional groups of phenolic compounds (O–H, C–H, C=C, C–C, C=O). These findings suggest that the analyzed byproducts can effectively serve as sources of bioactive compounds with potential applications in the formulation of functional foods and medicines. However, it is necessary to conduct compound identification and toxicity analysis to ensure the safety of these bioactive compounds.