Objective The incidence of obesity and other metabolic-related diseases has been gradually increasing. Multiple genetic as well as environmental factors play a significant role in the pathogenesis of these entities. Currently, the involvement of gut microbiota in metabolic processes has been acknowledged. This paper focuses on obesity, type 2 diabetes, and nonalcoholic fatty liver disease regarding their link with microbiome structure and its function. Materials and methods We analyzed literature available in PubMed, Embase, and Google Scholar databases regarding a linkage of metabolic-associated diseases and gut microbiota RESULTS: Gut microbiota plays a significant role in host metabolism. Depending on its composition; however, it may contribute to the development of metabolic-associated diseases. In this context, not only composition of gut microbiota is important, but also its activity. Short-chain fatty acids or lipopolysaccharides are crucial metabolites involved in maintaining metabolic balance. Conclusions Gut microbiota malfunctions might potentially induce obesity, type 2 diabetes, and nonalcoholic fatty liver disease.