Several functional properties have been attributed to soy protein hydrolysates (SPHs); however, their gut fermentation needs to be investigated. This study aimed to determine the effect of hypo-allergic pepsin-educed SPH on the growth of gut microbiota, SCFA and BCFA production in a pH-controlled, stirred, batch culture fermentation system compared with commercial SPH and soy protein isolate (SPI). The results showed that all substrates affected gut bacteria. SPH selectively increased the number of lactobacilli (log 9.61 to log 9.84) at 72-h fermentation, but not for bifidobacteria. This is in accordance with increased BCFAs yield of 15.54 ± 0.00 mm (isobutyrate) and 465.59 ± 1.42 mm (isovalerate). The gut microbial balance index (GMBI) of SPH was 0.23, thus suggesting its gut microbial modulation. Therefore, SPH has potential for modulation or balance of gut microbiota, which may be used as functional ingredient for emerging market of nutraceuticals and nutri-pharmaceutical industry.