Background <p>The intestinal microbiome and its metabolome shape key pathogenetic mechanisms of inflammatory bowel diseases and influence inflammatory activity, surgical outcomes and the risk of disease recurrence.</p> Objective <p>To summarize the evidence on the role of the intestinal microbiome and metabolome in the pathogenesis of inflammatory bowel diseases, to delineate their relevance in the surgical context and to outline the resulting therapeutic implications.</p> Material and methods <p>Selective literature review including experimental, translational and clinical studies.</p> Results <p>Preclinical and clinical studies demonstrate that genetic risk variants, a&#xa0;western diet and alterations in the composition and function of the intestinal microbiome and its metabolome constitute major determinants in the pathogenesis of inflammatory bowel diseases.</p> Discussion <p>Current evidence suggests that alterations of the intestinal microbiome and metabolome substantially contribute to the disease dynamics in inflammatory bowel diseases and shape both conservative and postoperative outcomes. Targeted modulation of the intestinal microbiome and metabolome could represent a&#xa0;promising approach for treating inflammatory bowel diseases and preventing recurrences.</p>