This review discusses the effects of short-chain fatty acids (SCFAs) and trimethylamine-N-oxide (TMAO) on metabolic diseases, focusing on non-alcoholic fatty liver disease (NAFLD) and cardiovascular disease, and suggests dietary modification as a promising therapeutic strategy. SCFAs, a product of fiber fermentation by microbiota, foster intestinal cell populations, upregulate mucin production, and secure the gut barrier. In contrast, TMAO, a microbiota-produced metabolite from choline, phosphatidylcholine, and l-carnitine, induces atherosclerosis by decreasing cholesterol clearance. An unmanageable abundance of TMAO is potentially harmful to patients with NAFLD owing to its ability to regulate the synthesis and transport of bile acids. The production of SCFAs and TMAO is strongly dependent on the microbial community; therefore, dietary modifications, such as reduction in meat intake, and prebiotic and probiotic consumption that can shape the gut microbiome are considered as promissing therapeutic approaches. This review focuses on well-known prebiotics, such as inulin, fructooligosaccharides, and β-glucan, and probiotics, such as VSL#3 mixture, Lactobacillus rhamnosus GG, Bifidobacterium, and Lactobacillus spp. These additives facilitate microbiota modification, gut homeostasis, intestinal barrier maintenance, and promotion of cholesterol excretion, which may protect the liver from steatosis, inflammation, and fibrosis. Controversial results from previous studies suggest that personalized approaches should be used for dietary modifications.