Inflammatory bowel disease (IBD) is a group of chronic gastrointestinal inflammatory conditions which can be life‐threatening, affecting both children and adults. Crohn's disease and ulcerative colitis are the two main forms of IBD. The pathogenesis of IBD is complex and involves genetic background, environmental factors, alteration in gut microbiota, aberrant immune responses (innate and adaptive), and their interactions, all of which provide clues to the identification of innovative diagnostic or prognostic biomarkers and the development of novel treatments. Gut microbiota provide significant benefits to its host, most notably via maintaining immunological homeostasis. Furthermore, changes in gut microbial populations may promote immunological dysregulation, resulting in autoimmune diseases, including IBD. Investigating the interaction between gut microbiota and immune system of the host may lead to a better understanding of the pathophysiology of IBD as well as the development of innovative immune‐ or microbe‐based therapeutics. In this review we summarized the most recent findings on innovative therapeutics for IBD, including microbiome‐based therapies such as fecal microbiota transplantation, probiotics, live biotherapeutic products, short‐chain fatty acids, bile acids, and urolithin A.