Soy isoflavone extracts are widely researched for their distinctive potential in contributing to various functional foods. The research work focuses on testing the toxicity of purified soy isoflavone extracts in mice models. With an agreement of the animal ethics, acute toxicity is firstly used to screen the effects of test compounds in mice for therapeutic purposes. Moreover, tests were conducted on BALB/c for estrogen in vivo and MCF7 for in vitro, screening active protection of liver cells, lipid peroxidation and scavenging free radicals 2,2-diphenyl-1-picrylhydrazyl (DPPH). Genistin and daidzin were found to be the two major compounds accounting for 47% and 35% of total purified soy isoflavones. The acute toxicity test results exhibited no effect against physiological accretion of BALB/c after 7-day administration with the given dose of 10 g/kgBW. Moreover, modified E-screen assay on MCF7 cells proved that the estrogen of isoflavone extracts induces cell proliferation by 15% compared with other non-steroid culture techniques. Therefore, this research contributes to helping researchers apply soy isoflavones in functional food, to alleviate the difficulties in menopausal symptoms for women in the future.SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13197-022-05491-4.