This study focuses on evaluating new methods for the green extraction of saponin compounds from Polygonatum cyrtonema Hua (PCH). This study utilized a combination of carboxylic acid-based natural deep eutectic solvents (NADES) and various extraction techniques including conventional heat reflux-, ultrasound-, and microwave-assisted extraction. The primary objectives were to assess total saponin yield, antioxidant capacity, and enzyme inhibition efficiency. Additionally, the solvents and extracts were evaluated for their antibacterial activity. Oil-in-water (O/W) emulsions of NADES extracts were also characterized and analyzed for stability. Results indicated that three NADES systems were effective in extracting saponins, with choline chloride and lactic acid (ChCl-LA) system being the most efficient. The ChCl:LA extract exhibited antimicrobial and antioxidant activities superior to conventional organic solvent extracts. Additionally, it demonstrated maximum inhibitory activity (IC50 values: 0.98 ± 0.03 and 1.46 ± 0.07 mg/mL, respectively) against α-glucosidase and α-amylase. The NADES extract as an aqueous phase significantly improved the stationarity of the O/W emulsion. Collectively, the study highlights the antimicrobial and technological advantages of NADES as a potential solvent for extracting saponin compounds from PCH.