Honey is a natural sweet element that bees make with flower nectar, revered for its distinct flavor, nutritional value, and potential health benefits. Chilean beekeeping has a diverse range of honey varieties, many of which are unique. The quillay (Quillaja saponaria Molina, soapbark tree) is a Chilean endemic tree whose honey has not been studied in depth. We characterized various Chilean honeys with different botanical origins, with a particular focus on quillay tree honey, analyzing its total phenolic and flavonoid content and its antioxidant activities. Cytotoxicity and hepatoprotective activity were also evaluated using HuH-7 cells. The Spearman correlation between the percentage of quillay pollen in the honey samples and the total phenolic content (R = 0.72; p < 0.05), plus the oxygen radical absorbance capacity, suggests that compounds from quillay contribute to the overall antioxidant capacity of honey. Unifloral quillay honey extracts also protect hepatic cells from oxidative damage induced by peroxyl radicals generated by AAPH. This analysis sheds light on the potential of quillay tree honey, underscoring its significance as a natural source of bioactive phenolic compounds with possible hepatoprotective effects.