The relationship between diet and the diversity and function of the intestinal microbiomeand its importance for human health is currently the subject of many studies. The type and proportionof microorganisms found in the intestines can determine the energy balance of the host. Intestinalmicroorganisms perform many important functions, one of which is participation in metabolicprocesses, e.g., in the production of short-chain fatty acids—SCFAs (also called volatile fatty acids).These acids represent the main carbon flow from the diet to the host microbiome. Maintainingintestinal balance is necessary to maintain the host’s normal health and prevent many diseases.The results of many studies confirm the beneficial effect of probiotic microorganisms on the balanceof the intestinal microbiome and produced metabolites, including SCFAs. The aim of this review is tosummarize what is known on the effects of probiotics on the production of short-chain fatty acidsby gut microbes. In addition, the mechanism of formation and properties of these metabolites isdiscussed and verified test results confirming the effectiveness of probiotics in human nutrition bymodulating SCFAs production by intestinal microbiome is presented.