Carotenoids are natural micronutrients found in plants and microorganisms, but not synthesized by animals. Carotenoids show various biological activities, including antioxidant properties, regulation of cell growth, and modulation of gene expression and immune responses. The rising global incidence of fatty liver disease (FLD) and obesity highlights the importance of carotenoids in chronic progressive conditions. Gut microbiota (GM) dysbiosis is associated with the development and progression of obesity and FLD due to the effects of metabolites such as lipopolysaccharide (LPS), bile acids (BAs), and short-chain fatty acids (SCFAs). Furthermore, GM may affect intestinal barrier integrity. This review evaluates the potential impact of carotenoids on GM and intestinal barrier function, and their subsequent effects on obesity and FLD. We searched through a wide range of databases, such as Web of Science, Scopus, EMBASE, and PubMed, to collect data for our non-systematic review of English literature. Carotenoids such as lycopene, zeaxanthin, fucoxanthin, capsanthin, astaxanthin, and lutein can regulate GM composition and improve obesity and FLD by affecting energy expenditure, food intake, lipid profile, liver fat deposition, liver enzymes, inflammatory markers, glucose homeostasis, and bile acids. These carotenoids improve obesity and FLD through GM metabolites such as SCFAs and LPS. Our findings show that dietary supplementation of lycopene, zeaxanthin, fucoxanthin, capsanthin, astaxanthin, and lutein can positively affect obesity and FLD by regulating GM and intestinal barrier integrity.