Despite the various treatment methods that exist for obesity, the most effective treatment for long-term weight control is bariatric surgery. Different surgical methods affect different mechanisms, such as appetite change, restriction of intake, and control of hunger. Divert food from the proximal part of the small intestine, food aversion, increased energy expenditure, malabsorption of macronutrients, and modifications of bile aside profiles and the gut microbiota. Gut microbiota plays an important role in maintaining human health. Dysbiosis usually has detrimental effects and may also have long-term consequences that lead to diseases or disorders, such as diabetes, obesity, and inflammatory bowel disease. While Firmicutes are abundant in the gut microbiota of obese individuals, Bacteroidetes are more abundant in individuals with normal weight. Thus, specific changes in the gut microbial composition are associated with obesity. The suggestion of growing evidence of bariatric surgery’s success is because of the procedure’s effect on the gut microbiota. Bariatric surgery changes the short-chain fatty acids composition by certain changes in the gut microbiota, thus affecting host metabolism, including intestinal hormone secretion and insulin sensitivity. Different methods of bariatric surgery alter the gut microbiota differently.