To address the grand challenges of valorizing agricultural biomass (AB) residues, processes such as the extraction of phytochemicals need to align with the principles of green chemistry and sustainability. In this regard, Natural Deep Eutectic Solvents (NaDESs) are being utilized to extract value-added compounds from AB, thanks to their biodegradability, costeffectiveness, and low toxicity. The objective of this research was to valorize bell pepper AB residues (stalks and leaves) through the extraction of glycosylated flavonoids with antioxidant activity. To achieve this, 24 NaDESs were designed based on choline chloride (ChCl) and various hydrogen bond donors, including carboxylic acids and alcohols. The NaDESs extraction capacities for total flavonoids and two model flavonoids, quercitrin (quercetin 3-Orhamnoside) (Q3O-R) and cynaroside (luteolin 7-O-glucoside) (L7O-G), were systematically evaluated. Two crucial extraction parameters, time (measured in seconds) and ultrasonic amplitude (measured in Watts), were optimized using a central composite rotatable design (CCRD). The high content of bioactive flavonoids present in pepper AB residues was demonstrated by using ChCl/ 1,6-hexanediol in a 1:1 molar ratio with 30 wt % water (10.31 ± 0.16 mg quercetin equivalent/g dry AB). The ultrasonic pulseassisted NaDES extraction method outperformed the results obtained with conventional hydroethanolic extraction. Therefore, NaDESs represent an efficient and greener alternative to conventional organic solvents for extracting value-added compounds, such as natural antioxidants, from resilient lignocellulosic AB residues.