The gut microbiota (GM) is referred to as the second gene pool of the human body and a commensal, symbiotic, and pathogenic microorganism living in our intestines. The knowledge of the complex interaction between intestinal microbiota and health outcomes is a novel and rapidly expanding the field. Earlier studies have reported that the microbial communities affect the cellular responses and shape many aspects of physiology and pathophysiology within the body, including muscle and bone metabolism (formation and resorption). GM influences the skeletal homeostasis via affecting the host metabolism, immune function, hormone secretion, and the gut-brain axis. The premise of this review is to discuss the role of GM on bone homeostasis and skeletal muscle mass function. This review also opens up new perspectives for pathophysiological studies by establishing the presence of a ‘microbiota-skeletal’ axis and raising the possibility of innovative new treatments for skeletal development.