Mitochondrial metabolism determines bone marrow hematopoietic stem cell (HSC) heterogeneity and influences their repopulation potential, though its embryonic origins remain unclear. We show that during the endothelial-to-hematopoietic transition in the mouse embryo, dynamic changes in mitochondrial activity drive the production of hematopoietic stem and progenitor cells (HSPCs) with differing potencies. Lowering mitochondrial activity in the aorta-gonad-mesonephros (AGM) by pharmacological or genetic means activates Wnt signaling to promote HSPC expansion. Further, mitochondrial membrane potential (MMP) gives rise to functional heterogeneity in HSPCs. In-vitro and in-vivo functional assays and single-cell transcriptomics showed that MMP HSPCs in the AGM are myeloid biased, with enhanced differentiation potential, whereas MMP HSPCs are lymphoid biased, with diminished differentiation potential. Mechanistically, low mitochondrial activity in HSPCs upregulates phosphoinositide 3-kinase signaling to promote differentiation. These insights into the initiation of metabolic heterogeneity could be leveraged to isolate the distinct HSPC subsets and to efficiently generate the desired lineages.