An understanding of mucosal immunity is essential for the comprehension of intestinal diseases that are often caused by a complex interplay between host factors, environmental influences and the intestinal microbiota. Not only improvements in endoscopic techniques, but also advances in high throughput sequencing technologies, have expanded knowledge of how intestinal diseases develop. This review discusses how the host interacts with intestinal microbiota by the direct contact of host receptors with highly conserved structural motifs or molecules of microbes and also by microbe-derived metabolites (produced by the microbe during adaptation to the gut environment), such as short-chain fatty acids, vitamins, bile acids and amino acids. These metabolites are recognised by metabolite-sensing receptors expressed by immune cells to influence functions of macrophages, dendritic cells and T cells, such as migration, conversion and maintenance of regulatory T cells and regulation of proinflammatory cytokine production, which is essential for the maintenance of intestinal homeostasis and the development of intestinal diseases, such as inflammatory bowel diseases. First interventions in these complex interactions between microbe-derived metabolites and the host immune system for the treatment of gastrointestinal diseases, such as modification of the diet, treatment with antibiotics, application of probiotics and faecal microbiota transplantation, have been introduced into the clinic. Specific targeting of metabolite sensing receptors for the treatment of gastrointestinal diseases is in development. In future, precision medicine approaches that consider individual variability in genes, the microbiota, the environment and lifestyle will become increasingly important for the care of patients with gastrointestinal diseases.