Disease progression in metabolic dysfunction-associated steatotic liver disease (MASLD) is driven by multiple mechanisms that act together in genetically predisposed subjects. Amongst others, the gut-liver axis plays a crucial role in the development and progression of MASLD. This inevitably involves the microbiome. The exact impact of the microbiome on MASLD is not yet fully understood, but the imbalance in gut microbiota (GM) can cause altered integrity of the intestinal epithelium, increased permeability of the intestinal barrier, and various harmful substances and metabolites secreted by the GM reaching the liver. The gut and liver interact bidirectionally through multiple molecules and products, such as nutrients, microbial antigens, metabolites, and bile acids (BAs), which affect both metabolism and immunity, thus controlling both gastrointestinal and liver health and disease. Understanding the factors that shape microbiome complexity may help improve prevention, diagnosis, and treatment in a precise and personalized manner. This review focuses on the recent data on the etiopathogenesis of MASLD linked to the gastrointestinal microbiome and looks critically into the research methods that should aim at comprehensively and accurately reflecting the true status of the GM.