Upon stem cell transition from quiescence to proliferation, mitochondrial biogenesis takes place, which is associated with increased mitochondrial oxidative stress and mitochondrial protein folding stress. SIRT3 and SIRT7 govern mitochondrial stress in stem cells. Damaged mitochondria can also be cleared by mitochondrial fusion and fission, and mitophagy. Accumulation of mitochondrial stress results in stem cell death due to DNA mutations and activation of the NLRP3 inflammasome, which is regulated by SIRT2. During aging, the expression of SIRT2, SIRT3, and SIRT7 reduces in stem cells, resulting in the dysregulation of the mitochondrial metabolic checkpoint and loss of stem cell maintenance.