Naive epiblast and embryonic stem cells (ESCs) give rise to all cells of adults. Such developmental plasticity is associated with genome hypomethylation. Here, we show that LIF–Stat3 signaling induces genomic hypomethylation via metabolic reconfiguration. Stat3-/-ESCs show decreased a-ketoglutarate production from glutamine, leading to increased Dnmt3aand Dnmt3bexpression and DNA methylation. Notably, genome methylation is dynamically controlled through modulation of a-ketoglutarate availability or Stat3 activation in mitochondria. Alpha-ketoglutarate links metabolism to the epigenome by reducing the expression of Otx2and its targets Dnmt3aand Dnmt3b. Genetic inactivation of Otx2or Dnmt3aand Dnmt3bresults in genomic hypomethylation even in the absence of active LIF–Stat3. Stat3-/-ESCs show increased methylation at imprinting control regions and altered expression of cognate transcripts. Single-cell analyses of Stat3-/-embryos confirmed the dysregulated expression of Otx2, Dnmt3aand Dnmt3bas well as imprinted genes. Several cancers display Stat3 overactivation and abnormal DNA methylation; therefore, the molecular module that we describe might be exploited under pathological conditions.