This work presents a new bioprocess process for the extraction of bioactive components from soy pulp by-product (okara) using an enzymatic technology that was compared to a conventional water extraction. Okara is rich in fiber, fat, protein, and bioactive compounds such as isoflavones but its low solubility hampers the use in food and fertilizer industry. After the enzymatic attack with endoproteases half of the original insoluble proteins were converted into soluble peptides. Linked to this process occured the solubilization of isoflavones trapped in the insoluble protein matrix. We were able to extract up to 62.5% of the total isoflavones content, specially aglycones, the more bioactive isoflavone forms, whose values rose 9.12 times. This was probably due to the increased solubilization and interconversion from the original isoflavones. In conclusion, our process resulted in the formulation of a new functional product rich in aglycones and bioactive peptides with higher antioxidant potency than the original source. Therefore, we propose that the enzymatic extraction of okara bioactive compounds is an advantageous tool to replace conventional extraction.