The demand for sustainable methods to extract bioactive compounds from native fruits is increasing. We evaluated the potential of natural deep eutectic solvents (NaDES) combined with ultrasound-assisted extraction (UAE) to recover phenolic compounds from Ugni molinae Turcz. (murta), a Chilean fruit with recognized ethnopharmacological and antioxidant value. Seven choline chloride-based NaDESs (M1–M7) were assessed and compared with conventional methanol: formic acid extraction (M8). The choline chloride: 1,2-propanediol system (1:2, M2) achieved the highest recovery of total phenolics (64.87 mg GAE/g) and flavonoids (35.38 mg QE/g), together with strong antioxidant activity (DPPH IC₅₀: 1.05 µg/mL; ORAC: 40,291 µmol TE/g). When comparing the different NaDES formulations (M1–M8), M8 displayed superior FRAP and ORAC values, although its phenolic and flavonoid yields were lower, reflecting differences in solvent selectivity. HPLC-DAD analysis further revealed that NaDES, particularly M5 (choline chloride: oxalic acid, 1:1), favored the extraction of flavonoid and anthocyanin-type compounds. Multivariate and PCA analyses showed distinct chemical profiles in NaDES extracts, forming two clusters apart from M8. Pearson correlation analysis linked antioxidant capacity with major flavonoids. Overall, NaDES combined with UAE represents an efficient, green strategy for selectively recovering bioactives, supporting applications in foods, nutraceuticals, and health products from Chilean native fruits.