To clarify the effects of soy protein (SP) and β-conglycinin (BC) on human gut microbiota, human stool samples, collected from four healthy volunteers, were incubated without (control) or with 3% (w/v) SP and BC at 37 °C for 24 h under anaerobic conditions. During incubation, the amount of dissolved protein decreased and that of ammonia increased, although indole content was lower in both SP and BC cultures than in control cultures. The degraded protein band pattern, obtained by sodium dodecyl sulphate-polyacrylamide gel electrophoresis, varied across individuals. Total organic acids tended to increase in amount in SP and BC cultures, with n-butyric acid levels increasing significantly (p < 0.05) in the BC culture. The gut microbiota were analysed using 16S rRNA (V4) gene amplicon sequencing. Genera regarded as butyrate producers, such as Roseburia, Butyricicoccus, and Faecalibacterium, were high in both SP and BC cultures, and the genera and amplicon sequence variants of butyrate producers varied across individuals. The incubation with SP and BC increased the superoxide anion radical scavenging capacity and ferric reducing power of the faecal cultures. As an invitro immunomodulatory activity, increased promotion of nitric oxide secretion in murine macrophage-like RAW264.7 cells was observed in the BC cultures. Overall, the effects of SP and BC were considered positive with respect to the host.