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Soybean is an important natural source of isoflavones, but their concentration is likely to be influenced by external factors, such as climatic conditions and soil tillage systems. However, there is minimal information about the effects of such external factors on the isoflavone concentration in soybeans grown in Europe. Therefore, in this study, field experiments were established in Romania to investigate the potential impacts of three different soil tillage systems—conventional, minimum tillage and no-tillage—on crop yields and the isoflavone concentration of soybeans for three experimental years, 2014–2016. Our experimental results indicated that the soil tillage systems had little impact on the soybean yields each year. However, the 2016 yield was found to be higher than the 2014 and 2015 yields under all three soil systems. For every experimental year, the higher yield was recorded by the conventional system, followed by the minimum tillage system and no-tillage system under first weed control (weed control two (wct2): S-metolaclor 960 g/L, imazamox 40 g/L and propaquizafop 100 g/L). Likewise, the soil tillage system did not have a significant influence on the total isoflavone concentrations. Nevertheless, we noticed some variations in the individual isoflavone concentration (daidzin, genistin, glycitin, daidzein, genistein) in each year. Altogether, the minimum tillage and no-tillage systems may be employed as a suitable soil tillage system in soybean farming without an impact on the total isoflavone.

Potential Impacts of Soil Tillage System on Isoflavone Concentration of Soybean as Functional Food Ingredients