Microbiota is the collectivity of microorganisms settling in the gut of humans and animals. The symbiotic interactions between microbiota and host are of essential physiological and pathophysiological importance. Unfavorable compositional and metabolic changes in the gastrointestinal microbiota (“dysbiosis”) are associated with the development and maintenance of several inflammatory disorders, including chronic inflammatory bowel disease (IBD). IBD-associated dysbiosis can be treated by the administration of antibiotics and of prebiotics/probiotics and by fecal microbiota transfer (FMT). It was found that treatment with antibiotics can harm beneficial microorganisms, leading to a changed composition of microbiota and therefore is no longer the first choice. Prebiotics are food ingredients that induce growth or activity of beneficial microorganisms. Probiotics include nonpathogenic living microorganisms that populate the gut. They have positive impacts on the balance of microbes and improve the absorption of micronutrients. Therefore, they may have a positive impact on the course of IBD. Recently, the effectiveness and safety of FMT as a novel therapeutic application have been demonstrated. A FMT involves the transplantation of fecal microorganisms from a healthy donor. FMT was administered in the form of capsules or suspensions and delivered by mouth, nasoduodenal tube, enema, or colonoscopy. Each method of administration carries its own set of risks, including adverse reactions to treatment, infection following the invasive administration procedure, and flare-ups of GI-related symptoms. Although further research is still needed to understand the relationship between dysbiosis of gut microbiota and extra- and intraintestinal inflammation, FMT is a promising approach to treat IBD.