Little is known about the spatio-temporal coordination of mitochondrial metabolism in multicellular organisms in situ. Using intravital microscopy in live animals, we here report that mitochondrial metabolism undergoes rapid and periodic oscillations under basal conditions. Notably, mitochondria in vivo behave as a network of functionally coupled oscillators, which maintain a high level of coordination throughout the tissue via the activity of gap junctions. These findings reveal a unique aspect of the relationship between tissue architecture and self-organization of mitochondrial metabolism in vivo.