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Background: Urinary excretion of isoflavones and their metabolites after the consumption of soybean meal (SBM) and fermented soybean meal (FSBM) biscuits was investigated in humans in a randomized double-blinded crossover clinical trial., Results: Aglycones were the most abundant metabolites in urine in both treatments. After FSBM consumption, total urinary excretion of aglycones and metabolites was 54% higher when compared to SBM biscuits. All metabolites were more rapidly excreted after FSBM biscuit consumption when compared to SBM biscuits. Urinary recovery of isoflavones was higher after FSBM biscuit consumption, reaching 67%. Women excreted higher amounts of colonic metabolites and lower amounts of aglycones than men. The prevalence of O-demethylangolensin-producer, equol-producer and nonproducer metabotypes was 56%, 11% and 36% after SBM consumption and 72%, 11% and 17% after FSBM consumption, respectively., Conclusions: Together, our findings indicate that fermentation improves isoflavone bioavailability and possibly reduces the impact of gut microbiota on the metabolism of isoflavones. © 2020 Society of Chemical Industry., (© 2020 Society of Chemical Industry.)