The ability of stem cells for self-renewing, differentiation, and regeneration of injured tissues is believed to occur via the hormetic modulation of nuclear/ mitochondrial signal transductions. The evidence now indicates that in damaged tissues, the mitochondria set off the alarm under oxidative stress conditions, hence they are the central regulators of stem cell fate decisions. This review aimed to provide an update to a broader concept of stem cell fate in stress conditions of damaged tissues, and insights for the mitochondrial hormesis (mitohormesis), including the integrated stress response (ISR), mitochondrial dynamics, mitochondria uncoupling, unfolded protein response, and mitokines, with implications for the control of stem cells programing in a successful clinical cell therapy.