Life on Earth is dictated by circadian changes in the environment, caused by the planet’s rotation around its own axis. All forms of life have evolved clock systems to adapt their physiology to the daily variations in geophysical parameters. The intestinal microbiome serves as a signaling hub in the communication between the host and its environment. We recently discovered that the microbiota undergoes diurnal oscillations in composition and function, and that these oscillations are required for metabolic homeostasis of the host. Here, we highlight these findings from the perspectives of microbial system stability and meta-organismal metabolic health. We also discuss the contribution of nutrition and biotic interventions on diurnal processes of the microbiota and their potential involvement in diseases commonly associated with circadian disruption.