Soybean is a pulse which has considerable nutritional value due to its high protein, fibers and polyunsaturated fatty acid (PUFA) contents. It also contains phytoestrogenic compounds that definitely hinder its recommendation for general consumption. Contrary to ancient times, when soybeans were boiled, modern commercial soy foods can contain up to 150 mg/100g of estrogenic isoflavones. Interestingly, current estimations of isoflavone intake in the literature do not distinguish between the origins of soy food, i.e., whether it is homemade or commercial. As a result, the isoflavone exposure in Asian countries may well be overestimated. This study aims to demonstrate, based on step-by-step monitoring of isoflavones, that traditional and domestic treatments, leveraging isoflavones water-solubility, can indeed significantly reduce their content in soy foods. Indeed, when compared to commercial foods, the isoflavone content was found to be 20, 2.6, 4.5 and 9.8 times lower in “homemade” soy juice, tofu, tempeh and miso, respectively. Additionally, water soaking was found to reduce the isoflavones levels in soy-textured proteins by more than 70%. Hence, this simple process has the potential to help drastically reduce overall xenoestrogens exposure. This study could serve as a basis for establishing the isoflavones Reference Dose and issuing food safety guidelines.