The extraction efficiency, recovery, quantification, and stability of isoflavones (daidzein, genistein and puerarin) from the wastes /by-products of kudzu roots and soy molasses were evaluated by using natural deep eutectic solvents (NADESs) coupled with ultrasound-assisted extraction. The NADES extraction was compared with the conventional Soxhlet extraction technique, and the extracted isoflavones were quantified using HPLC-UV/Vis. Results showed extractability of puerarin to be significantly increased (p < 0.0001) in proportion to the increased water concentration of NADES (9.7 ± 0.2, 12.6 ± 0.2, and 14.8 ± 0.3 mg/g in NADESs containing 10%, 20%, and 30% water, respectively). Despite having less isoflavone content, kudzu roots and soy molasses extracts obtained using NADES exhibited higher antioxidant activity when compared with methanolic extracts. Further, NADES extracts also markedly reduced the degradation degree of isoflavones. The results of this investigation support the use of green extraction techniques to obtain value-added components like isoflavones from wastes/by-products like that of kudzu roots and soy molasses, which are envisaged to find future potential applications in the food and pharmaceutical industries. Display omitted •Green extraction technique (UAE) with NADES was employed for extraction.•Water concentration of NADES directly influenced the extractability.•Sample-to-NADES volume directly influenced the extractability.•NADES extracts showed higher antioxidant activity and storage stability.•Extraction of isoflavones using NADES was more effective than conventional methods.