Peumus boldus Mol., is a Chilean medicinal tree used for gastrointestinal and liver diseases. Such medicinal properties are associated with the presence of bioactive flavonoids and aporphine alkaloids. In this study, a new green and efficient extraction method used seven natural deep eutectic solvents (NADES) as extraction media. The extraction efficiency of these NADES was assessed, determining the contents of boldine and total phenolic compounds (TPC). Chemical profiling of P. boldus was done by high-performance liquid chromatography coupled to photo diode array detector and electrospray ion-trap mass spectrometry (HPLC-PDA-ESI-IT/MS) and electrospray ionization quadrupole time-of-flight high-resolution mass spectrometry (HPLC-ESI-QTOF-MS). Among the NADES tested, NADES4 (choline chloride-lactic acid) and NADES6 (proline-oxalic acid) enable better extraction of boldine with 0.427 ± 0.018 and 2.362 ± 0.055 mg of boldine g⁻¹ of plant, respectively. Extraction of boldine with NADES4 and NADES6 was more efficient than extractions performed with methanol and water. On the other hand, the highest TPC were obtained using NADES6, 179.442 ± 3.79 mg of gallic acid equivalents (GAE g⁻¹). Moreover, TPC in extracts obtained with methanol does not show significant differences with NADES6. The HPLC-PAD-MS/MS analysis enable the tentative identification of 9 alkaloids and 22 phenolic compounds. The results of this study demonstrate that NADES are a promising green extraction media to extract P. boldus bioactive compounds and could be a valuable alternative to classic organic solvents.