Intestinal microbiota, and their mutual interactions with host tissues, are pivotal for the maintenance of organ physiology. Indeed, intraluminal signals influence adjacent and even distal tissues. Consequently, disruptions in the composition or functions of microbiota and subsequent altered host–microbiota interactions disturb the homeostasis of multiple organ systems, including the bone. Thus, gut microbiota can influence bone mass and physiology, as well as postnatal skeletal evolution. Alterations in nutrient or electrolyte absorption, metabolism, or immune functions, due to the translocation of microbial antigens or metabolites across intestinal barriers, affect bone tissues, as well. Intestinal microbiota can directly and indirectly alter bone density and bone remodeling. Intestinal dysbiosis and a subsequently disturbed gut–bone axis are characteristic for patients with inflammatory bowel disease (IBD) who suffer from various intestinal symptoms and multiple bone-related complications, such as arthritis or osteoporosis. Immune cells affecting the joints are presumably even primed in the gut. Furthermore, intestinal dysbiosis impairs hormone metabolism and electrolyte balance. On the other hand, less is known about the impact of bone metabolism on gut physiology. In this review, we summarized current knowledge of gut microbiota, metabolites and microbiota-primed immune cells in IBD and bone-related complications.