Purpose: Inflammatory bowel disease (IBD) encompasses two main conditions - Crohn’s disease (CD) and ulcerative colitis (UC). Its mechanism is vastly unknown but genetics, environmental factors, and the gut microbiome are thought to play a role. While dysbiosis is thought to be a feature of IBD, its exact role in the pathogenesis of IBD is unclear. Methodology: Relevant studies were identified through searching Medline and Embase from database inception to July 2023. Only gastrointestinal microbiome studies comparing IBD human patients with healthy controls (HC), performed on faecal, mucosal biopsy, saliva, or oral swab samples were examined. Studies were excluded if they included ≤10 IBD patients, did not compare IBD to HC, reported on IBD with other gastrointestinal infections, all were taking IBD medications, or included post-operative bowel resection patients. Results: Of 75 identified observational studies, most reported reduced alpha and beta diversity in IBD, but this was more prevalent in CD than UC. There was depletion of protective butyrate producing Firmicutes bacteria including Faecalibacterium (specifically F. prausnitzii), Eubacteria, Roseburia, Lachnospiraceae, Ruminococcaceae (mainly R. bromii). There was also decreased Bacteroidetes phylum in IBD, with depletion of Bacteroides genus in CD but not in UC. There was increased Proteobacteria and its family Enterobacteriaceae in IBD. Conclusions: The gut microbiome in IBD demonstrated reduced biodiversity, more pronounced in CD, with increased pathogenic and reduced beneficial bacteria, however, this is only part of the pathogenesis of IBD with its full mechanism yet to be elucidated.