In recent years, the gut microbiota has become an integral research topic in human health owing to its impact on digestion, immunity, metabolic processes, and mental health. The possibilities of microbiome treatment have increased interest in dietary approaches, with a special focus on the intake of fermented foods. This has revived some of the most profound and practical constructs derived from food therapy in Chinese medicine (CM), where food therapy, along with fermented options, actively preserves health and prevents disease. In CM, the spleen and stomach system refers to the postnatal foundation of the body, which controls the processes of chewing, nutrient assimilation, and energy production (qi). The balance between intestinal and overall health is the foundation of psychosomatic well-being and is of utmost importance. Fermented foods can boost the spleen, alleviate stagnant food syndrome, dispel excess fluids, enhance protective functions, and strengthen the immune system. This review aimed to integrate the conceptual and clinical paradigms of CM with those of Western medicine, focusing on the role of fermented foods in gut microbiota regulation. This article discusses prominent fermented foods in CM and their classical functions, alongside the currently available peer-reviewed literature (published within the last 7 years) on their impact on gut flora and other clinical outcomes. Mechanistic considerations regarding the production of probiotics and other active metabolites, such as short-chain fatty acids, and the modulation of the intestinal barrier are discussed. This review also examines multidisciplinary approaches to dietary customs worldwide and outlines the clinical applications of these findings in the context of chronic disease management and gastrointestinal health.