Muscle stem cells (MuSCs) provide a constant regenerative capacity to the skeletal muscle owing to their capacity to recapitulate a myogenic program upon muscle lesion. Alterations of MuSC myogenic capacity are associated to muscle loss with age, but also debilitating diseases such as myopathies. A metabolic program centered around mitochondria is regulated in muscle stem cells (MuSCs) to support myogenesis. Yet, our knowledge of the signaling pathways controlling a metabolic remodeling in MuSCs is still fragmental. Here, we focus on NUAK1, a serine/threonine kinase related to the metabolic regulator AMPK, and whose primary functions encompass the regulation of mitochondrial metabolism to support neuronal development. We report for the first time that NUAK1 plays a role in the regulation of the MUSC fate program. We generated a conditional and inducible mouse model to investigate the impact of NUAK1 loss on MuSC. Using this mouse model, we demonstrated that NUAK1 expression is required for muscle regeneration capacity and identified that NUAK1 controls sequential aspects of the myogenic program, i.e., MuSC proliferation and differentiation, and MuSC self-renewal. A transcriptomic analysis pointed out a deregulation of metabolic pathways, which we could confirm using myogenic assays in MuSCs. We finally performed an unbiased analysis of the mitochondrial proteome to identify a post-translational metabolic signature of NUAK1 deletion in MuSCs. Altogether, our work proposes a novel kinase pathway linking metabolic regulation and stem cell fate.