Antibiotics lead to increased susceptibility to colonization by pathogenic organisms, with different effects on the host-microbiota relationship. Here, we show that metronidazole treatment of specific pathogen-free (SPF) mice results in a significant increase of the bacterial phylum <i>Proteobacteria</i> in fecal pellets. Furthermore, metronidazole in SPF mice decreases hind limb muscle weight and results in smaller fibers in the tibialis anterior muscle. In the gastrocnemius muscle, metronidazole causes upregulation of <i>Hdac4</i> , <i>myogenin</i> , <i>MuRF1</i> , and <i>atrogin1</i> , which are implicated in skeletal muscle neurogenic atrophy. Metronidazole in SPF mice also upregulates skeletal muscle <i>FoxO3</i> , described as involved in apoptosis and muscle regeneration. Of note, alteration of the gut microbiota results in increased expression of the muscle core clock and effector genes <i>Cry2</i> , <i>Ror</i> - <i>β</i> , and <i>E4BP4</i> . <i>PPARγ</i> and one of its important target genes, <i>adiponectin</i> , are also upregulated by metronidazole. Metronidazole in germ-free (GF) mice increases the expression of other core clock genes, such as <i>Bmal1</i> and <i>Per2</i> , as well as the metabolic regulators <i>FoxO1</i> and <i>Pdk4</i> , suggesting a microbiota-independent pharmacologic effect. In conclusion, metronidazole in SPF mice results in skeletal muscle atrophy and changes the expression of genes involved in the muscle peripheral circadian rhythm machinery and metabolic regulation.