In vitro gut fermentation systems are relevant tools to study health benefits of foodstuffs. Most of them are commonly used to investigate the degradation of nutrients or the development of gut flora. Using these models, strong cytotoxic effects of the resulting samples on cultured cells were observed. Hence, the aim of the present study was to develop a modified in vitro fermentation model that simulates the whole digestive tract and generates fermented samples that are suitable for testing in cell culture experiments. Wholemeal wheat flour (wwf) was digested and fermented in vitro with a fermentation model using different ox gall concentrations (41·6 and 0·6 g/l). The resulting fermentation supernatants (fs) were characterised for metabolites and biological effects in HT29 cells. The fermentation of wwf increased chemopreventive SCFA and decreased carcinogenic deoxycholic acid (DCA). The strong cytotoxic effects of the fs, which were partly due to cholic acid and DCA, were diminished by lowering the ox gall concentration, allowing the use of the samples in cell culture experiments. In conclusion, an in vitro digestion model, which can be used to study the effects of foodstuffs on chemoprevention and gut health in colon cells, is introduced and its physiological relevance is demonstrated.