The effect of long-term exposure of goldfish to dietary genistein and diadzein on the concentrations of plasma sex steroids (testosterone (T), 17β-estradiol (E2)) and the gonadosomatic index (GSI) was assessed. The study was conducted on four groups for a period of 2 years, from the age of 20 weeks to first spawning. Four doses of genistein and diadzein were applied in the feed: genistein: 0 µg/g, diadzein: 0 µg/g (control group); genistein: 24.26 µg/g, diadzein: 21.7µg/g (diet 1); genistein: 51.55 µg/g, diadzein: 46.13 µg/g (diet 2); and genistein: 75.83 µg/g, diadzein: 67.82µg/g (diet 3). Throughout the experiment, there were no significant dose- or time-related effects of genistein and diadzein contents on the T level in both sexes. Furthermore, at the highest genistein and diadzein contents, there was an elevating plasma concentration of E2 at all sampling points (p < 0.05) and a time-related effect occurred (p < 0.05). Although the E2 concentrations in the plasma of female, throughout the experiment, were higher than in males, at the last sampling, the plasma concentrations of E2 reduced among females and became lower than that in males. The effects of isoflavone content were found on GSI of females at the fourth and fifth sampling among the treatments. Isoflavone contents also affect GSI of males at the second, fourth and the last sampling. Our findings suggest that overall genistein and diadzein exposure in early life stages can cause alterations in the reproductive organs and influence sex steroidogenesis.