Precise matching of energy supply with demand requires delicately balanced control of the enzymes involved in substrate metabolism. In response to a change in substrate supply, the nonlinear properties of metabolic control may induce complex dynamic behavior. Using confocal imaging of flavoprotein redox potential and mitochondrial membrane potential, we show that substrate deprivation leads to subcellular heterogeneity of mitochondrial energization in intact cells. The complex spatiotemporal patterns of redox and matrix potential included local metabolic transients, cell-wide coordinated redox transitions, and propagated metabolic waves both within and between coupled cells. Loss of metabolic synchrony during mild metabolic stress reveals that intra- and intercellular control of mitochondrial function involves diffusible cytoplasmic messengers.