This study evaluates the concentration effect of green tea (GT), black tea (BT), and coffee (CF) polyphenols in set yogurt syneresis and its physicochemical attributes during refrigerated storage. All polyphenol-added yogurts showed a significantly lower (p < 0.05) syneresis than the control. High polyphenol concentrations significantly reduced syneresis, except in CFY, indicating that the percentage of syneresis reduction depends on the polyphenol type and its concentration. Treated yogurts showed a significantly higher (p < 0.05) viscosity than the control, indicating polyphenol–milk–protein matrix formation. In conclusion, adding natural polyphenols reduces syneresis in set yogurt while maintaining its physicochemical properties.