The microbiome has a major impact on human physiology and plays a critical role in enhancing or impairing various physiological functions such as regulation of the immune system, metabolic activities, and biosynthesis of vitamins and hormones. Variations in the gut microbial community play a critical role in both health and disease. Regulation of calcium and bone metabolism, as well as cellular functions such as proliferation, apoptosis, differentiation, and immune modulation, are among the known effects of vitamin D. These biological functions are primarily carried out through the binding of vitamin D to the vitamin D receptor (VDR), a member of the nuclear receptor superfamily. The immunomodulatory properties of vitamin D suggest that this molecule plays an important role in various diseases. Maintenance of immune homeostasis appears to occur in part through the interaction of the gut microbiota with vitamin D. Increasing evidence points to the central role of vitamin D in maintaining mucosal barrier function, as vitamin D deficiency has been associated with disruption of gut barrier integrity, translocation of bacteria into the bloodstream, and systemic inflammation. In parallel, a bidirectional interaction between vitamin D and the gut microbiota has been demonstrated as data show upregulation of intestinal VDR expression and downregulation of inflammatory markers in response to fermentation products. The aim of this review is to provide an overview of the evidence of a link between the gut microbiome and vitamin D, with a focus on data from experimental models and translational data from human studies related to vitamin D-induced changes in gut microbiota composition.