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Soy is a growing protein source; however, the isoflavones it contains are of concern, as they exhibit estrogenic activities whose toxicological limits might be exceeded. Reducing their concentrations to safe levels while preserving nutritional quality in soy foodstuffs is therefore a matter of public health. The main objective of this paper is to develop at pilot scale a process for isoflavones’ extraction from soybeans, and to show its feasibility and efficiency. The study was conducted by first optimizing the previously obtained laboratory treatment key factors. These data were then transposed to the pilot level. Finally, the process was adjusted to technical constraints which appeared at pilot scale: the mandatory use of drenching and the exploration of granulometry analysis. The involved steps were validated by monitoring the genistein and daidzein content variations through statistical analysis of the data of an ELISA and a Folin–Ciocalteu assay. Additionally, isoflavones’ recovery from treatment waters for their valorisation and the water cleaning by means of filtration, centrifugation and resin adsorption were carried out. The results showed that the most successful pilot treatment developed involved soybean dehulling, drenching, washing and drying and almost halved isoflavones while preserving the main nutritional characteristics. A combination of techniques led to almost complete recovery of isoflavones from process waters.