Soyabean intake is inversely correlated with risks of several chronic diseases in human. Phytochemicals and in particular phenolic acids, flavonoids and isoflavonoids compounds present in soyabean seeds may be partially responsible for these health benefits through their antioxidants activity. In a pot experiment, soyabean plants were grown on sandy media and irrigated with Hoagland solution as inorganic treatment or grown under one of the three levels of compost, i.e. 25, 50 and 75%, alone or in a mixture with multibioorganic. Individual phenolic acids, quercetin, genistein and daidzein in seeds were quantified by HPLC. Changes in the levels of individual phenolics and less value of quercetin under various compost levels resulted in insignificant lower values of total phenolics and total flavonoids compared with inorganically grown seeds. Adding multi-bioorganic to 50 or 75% compost treatments produced great enhancement effects on the total phenolic, flavonoid, protocatechuic acid, p-hydroxybenzoic acid, chlorogenic acid, caffeic acid, quercetin, genistein and daidzein contents compared with the other treatments. The most enhancement effect was exhibited for phenolic acids, quercetin and genistein. Addition of multi-bioorganic to 50% compost treatments resulted in 68 and 40% increases in quercetin and genistein, respectively, compared with the inorganic treatment, as well as 90 and 47% increases, respectively, compared with 50% compost alone. The highest values of antioxidant activity was determined in soyabean seeds grown under 50 and 75% compost, especially when mixed with bioorganic. Using either 50 or 75% compost in a mixture with bioorganic caused increases in antioxidant activity, varying between 25 and 60% when compared with other inorganic and compost alone treatments. Bioorganic fertilizers play a role in determining antioxidant activity and phenolic metabolites of soyabean seeds.