Soybeans are mainly used for food and biodiesel production. It is estimated that soy crops worldwide will leave about 651 million metric tons of branches, leaves, pods, and roots on the ground post-harvesting in 2022/23. These by-products might serve as largely available and cheap source of high added-value metabolites, such as flavonoids, isoflavonoids, and other phenolic compounds. This work aimed to explore green approaches based on the use of pressurized and gas expanded-liquid extraction combined with natural deep eutectic solvents (NADESs) to achieve phenolic-rich extracts from soy by-products. The total phenolic and flavonoid contents of the generated extracts were quantified and compared with conventional solvents and techniques. Pressurized liquid extraction (PLE) with choline chloride/citric acid/water (1:1:11 – molar ratio) at 120°C, 100 bar, and 20 min, resulted in an optimized condition to generate phenolic and flavonoid-rich fractions of soy by-products. The individual parts of soy were extracted under these conditions, with their metabolic profile obtained by UHPLC-ESI-QToF-MS/MS and potential antioxidant properties by ROS scavenging capacity. Extracts of soy roots presented the highest antioxidant capacity (207.48 ± 40.23 mg AA/g), three times higher than soybean extracts (68.96 ± 12.30). Furthermore, Hansen solubility parameters (HSPs) were applied to select natural hydrophobic deep eutectic solvents (NaHDES) as substituents for n-heptane to defat soybeans. Extractions applying NaHDES candidates achieved a similar yield and chromatography profile (GC-QToF-MS) to n-heptane extracts.