BACKGROUNDThe aim of this study was to investigate the effect of lactic fermentation on soy protein gastrointestinal digestive pattern and the influence of protein digesta on human faecal microbiota. Soymilk and soy yogurt were prepared in this study and a novel in vitro dynamic gastrointestinal model was employed to simulate gastric and duodenum digestions. Particle size, sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS‐PAGE), and peptide content were monitored at the end of duodenum tract.RESULTSIngestion of soy yogurt allowed a rapid drop in pH from 7.0 to 5.0 at simulated duodenal digestion (0–30 min), and resulted in a loss in soluble protein content compared to that of soymilk. The electrophoretic pattern between soymilk and soy yogurt exerted distinctive differences at early stages of duodenal digestion (0–60 min) and resulted in different peptide contents (180 min). Soy yogurt duodenal digesta collected at 180 min (D180), by co‐fermentation with human intestinal flora distribution, allowed a higher population in Bifidobacterium spp., Lactobacillus/Enterococcus spp. and Streptococcus/Lactococcus spp., whereas soy yogurt D30 resulted in lower population in Clostridium and Escherichia coli compared to samples co‐fermented with soymilk digesta.CONCLUSIONThe results demonstrated lactic fermentation of soy protein modulated human intestinal microflora and might relate to the different protein digestive behaviours. © 2020 Society of Chemical Industry