mtDNA depletion syndrome (MDS) is an important and expanding human disease, typically associated with early onset myopathy and muscular dysfunction. The molecular mechanisms underlying metabolic alterations, and their impact on disease progression remain largely uncharacterized in vivo. Here, we examine a conditional mouse model of mtDNA depletion in skeletal muscle which results in biochemical, histologic and phenotypic consequences characteristic of human MDS. Although previous in vitro studies suggest that mitochondrial dysfunction is associated with enhanced glycolysis, an integrated metabolomics analysis indicated an unexpected signature of reduced glycolysis in both myopathic mice, as well as patient muscle biopsies. The decrease in glycolysis was mediated by loss of constitutive Hif1alpha signaling, down-regulation of the purine nucleotide cycle enzyme AMPD1, and activation of AMPK. In vivo metabolic analysis using 13C-isotope tracing in mice indicated that lactate, and not glucose, is a major contributor to mitochondrial metabolites in mutant mice. Strikingly, mutant mice are dependent on lactate utilization for survival, and pharmacologic inhibition of lactate utilization rapidly compromised the life span of myopathic mice. Our results demonstrate an unexpected metabolic compensation in MDS, which implicates lactate as a key nutrient that regulates disease progression.