This work aimed to develop a novel methodology based on aqueous micellar systems (AMS), for producing soy protein concentrates (SPC) from soybean flour and recovering high-valuable bioactive compounds as by-products. Ethoxylated aliphatic alcohols Tergitol 15-S-7 and Tergitol 15-S-9, non-toxic and biodegradable sur-factants, were selected to form the AMS. The methodology consisted of an extractive stage of soybean flour with AMS, which rendered both a pellet, i.e., the SPC, and a supernatant containing the extracted bioactive com-pounds. The latter was further heated above the cloud point temperature, thus resulting in a biphasic system formed by a micelle-rich phase (MP) and an aqueous phase (AP). Obtained SPC showed a noticeable loss (similar to 90%) of trypsin inhibitor activity, a total protein content close to 60%, soluble protein amounts varying from 19% to 34%, and remarkable released (by simulated digestion) antioxidant and antihypertensive activities. Those in-dicators are similar to or even better than those corresponding to SPC from the classical acid-extraction method. The AMS also exhibited an enhanced efficiency for extracting antinutrients such as non-digestible oligosaccha-rides, trypsin inhibitors, and lectins mostly recovered at the AP and separated from isoflavones, which were concentrated and isolated at the MP. The recovery of all the mentioned bioactive compounds, whether beneficial or undesirable, broadens their uses in research, food, and pharmacological fields.This successful performance, simplicity, scalability, and sustainability make the proposed AMS-based extraction a powerful tool for processing plant derivatives and valorizing their by-products.