Bowman–Birk inhibitor (BBI) from soyabeans is a naturally occurring protease inhibitor with potential anti-inflammatory and chemopreventive properties within the gastrointestinal tract (GIT). In a previous paper, we reported that significant amounts of BBI-related proteins reach the terminal ileum functionally and biologically active. We have now investigated: (a) if soyabean BBI is biotransformed by faecal microbiota which would reduce its potential colorectal chemopreventive properties and (b) the potential influence of this protease inhibitor on the modulation of faecal microbiota. In vitro incubation studies of native soyabean BBI at a physiological level (93 μm) with mixed faecal samples of pigs for 24 h at 37°C demonstrated that BBI remains active and its intrinsic trypsin and chymotrypsin inhibitory activities were not significantly influenced by the enzymic or metabolic activity of faecal microbiota. Soyabean BBI did not affect the growth of the different bacterial groups studied (lactobacilli, bifidobacteria, bacteroides, coliforms, enterobacteria, clostridia and total anaerobes). It was concluded that protease inhibitory activities, intrinsically linked to the chemopreventive properties of soyabean BBI, were largely unaffected by faecal microbiota in vitro. BBI retains significance, therefore, as a bioactive compound in the human GIT.