Valorization of onion peel waste, considered to be a rich source of polyphenolic compounds, by employing green extraction techniques is the need of the hour. The aim of the present study was to optimize the microwave-assisted extraction of bioactive phenolic compounds from onion peel wastes employing ChCl:Urea:H 2O deep eutectic solvent. Microwave power (100–200–300 W), time (5–15–25 min) and liquid to solid ratio (40:1–50:1–60:1) were studied as the major parameters affecting the extraction efficiency. A Box–Behnken design was adopted including 17 experiments with five centre points. The optimum conditions determined were 100 W microwave power, 15.03 min irradiation time and 54.97 mL g −1 liquid to solid ratio. Under the MAE optimized conditions, the recovery of TPC and FRAP were 80.45 (mg GAE g −1 dw) and 636.18 (µmol AAE g −1 dw), respectively. Morphology of onion peels before and after DES extraction were also studied to gain an insight in the effect of microwave irradiations on the biomass.