Dietary fiber usually comes associated with phenolic compounds either trapped in a network formed by indigestible polysaccharides or, in some cases, bound to this matrix by covalent bonds. This natural association protects some phenolic compounds during their journey through the gastrointestinal tract, reaching the colon, where most polysaccharides undergo fermentation, weakening the matrix and promoting the release of these compounds to exert benefits by modulating intestinal function. Unfortunately, there are still difficulties in investigating the impact of the human microbiota on the release of phenolic compounds from the indigestible fraction and on their effects on the intestinal epithelium. In this study, grape pomace skin was subjected to in vitro digestion to obtain an indigestible fraction, which was further incorporated into SHIME bioreactors with human colonic microbiota. Throughout these stages, we monitored the release of phenolic compounds using HPLC-DAD. We determined the impact of a phenolic-rich indigestible fraction on the fermentative capacity of human microbiota by measuring the short-chain fatty acids (SCFA) levels and the effect of the resulting colonic ferments on the barrier properties of differentiated monolayers of Caco-2 cells by monitoring the transepithelial electrical resistance and the transcriptomic profile by RNA sequencing. Our results indicated that digestive processing sequentially increases the release of phenolic compounds and that colonic fermentation releases even more phenolic compounds trapped in the polysaccharide network. Unexpectedly, neither the phenolic-rich nor the depleted fractions increased SCFA levels in the colonic microbiota. Despite the lack of effect on the microbial community, the phenolic-rich ferments had a positive impact in the manner that monolayers of Caco-2 cells adapted better to repeated exposures with the ferments compared with phenolic-depleted ferments. In addition to his subtle difference, Caco-2 cells exposed to phenolic-rich ferments showed a remarkable increase in proteins associated with tight junctions, like claudin-3, -4, -15 and − 19, other proteins that connect the cytoskeleton with tight junctions, such as VASP (Ena/vasodilator-stimulated phosphoprotein) and CGNL1 (cingulin), supporting the idea that phenolic-rich ferments strengthened intercellular communication. In addition to this finding, we observed significant decreases in the transcription of genes encoding apical ion channels, such as CFTR, and the basolateral Na + /K + /Cl − cotransporter, both of which are relevant to intestinal chloride secretion and therefore may reduce fluid loss by the gut. In conclusion, our data support the positive impact of a subset of phenolic compounds that reach the colon, independent of SCFA levels. To achieve this finding in a biologically relevant context, we had to process grape pomace through physiological processes of digestion and fermentation. The latter stage was performed in a realistic colonic environment with human microbiota. The transcriptomic profile induced by the phenolic-rich ferments was observed following repeated exposures, a characteristic that warrants exploration of experimental designs to simulate dietary habits.