The present study aimed at evaluating the effectiveness of different natural deep eutectic solvents (NADES) on the extraction of phenolic compounds from Lavandula pedunculata subsp. lusitanica (Chaytor) Franco, on the antioxidant activity, and acetylcholinesterase (AChE), butyrylcholinesterase (BChE) and tyrosinase (Tyr) inhibitory capacities. Ten different NADES were used in this research and compared with conventional solvents. Ultrasound-assisted extraction (UAE) for 60 min proved to be the best extraction condition, and proline:lactic acid (1:1) and choline chloride:urea (1:2) extracts showed the highest total phenolic contents (56.00 ± 0.77 mgGAE/gdw) and antioxidant activity [64.35 ± 1.74 mgTE/gdw and 72.13 ± 0.97 mgTE/gdw in 2.2-diphenyl-1-picrylhydrazyl (DPPH) and 2.2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) methods, respectively]. These extracts also exhibited enzymes inhibitory capacity particularly against Tyr and AChE. Even so, organic acid-based NADES showed to be the best extractants producing extracts with considerable ability to inhibit enzymes. Twenty-four phenolic compounds were identified by HPLC-HRMS, being rosmarinic acid, ferulic acid and salvianolic acid B the major compounds. The results confirmed that the combination of UAE and NADES provide an excellent alternative to organic solvents for sustainable and green extraction, and have huge potential for use in industrial applications involving the extraction of bioactive compounds from plants.