Abstract Healthy aging can be promoted by enhancing metabolic fitness and physical capacity ( 1, 2 ). Mitochondria are chief metabolic organelles with strong implications in aging ( 3–8 ). In addition to their prominent role in bioenergetics, mitochondria also coordinate broad physiological functions by communicating to other cellular compartments or distal cells using multiple factors ( 9, 10 ), including peptides that are encoded within their own independent genome ( 11, 12 ). However, it is unknown if aging is actively regulated by factors encoded in the mitochondrial genome. MOTS-c is a mitochondrial-encoded peptide that regulates metabolic homeostasis ( 13, 14 ), in part, by translocating to the nucleus to regulate adaptive nuclear gene expression in response to cellular stress ( 15–17 ). Here, we report that MOTS-c is an exercise-induced mitochondrial-encoded peptide that significantly enhanced physical performance when administered to young (2 mo.), middle-aged (12 mo.), and old (22 mo.) mice. In humans, we found that endogenous MOTS-c levels significantly increased in response to exercise in skeletal muscle (11.9-fold) and in circulation (1.5-fold). Systemic MOTS-c treatment in mice significantly enhanced the performance on a treadmill of all age groups (~2-fold). MOTS-c regulated (i) nuclear genes, including those related to metabolism and protein homeostasis, (ii) glucose and amino acid metabolism in skeletal muscle, and (iii) myoblast adaptation to metabolic stress. Late-life (23.5 mo.) initiated intermittent MOTS-c treatment (3x/week) improved physical capacity and trended towards increasing lifespan. Our data indicate that aging is regulated by genes that are encoded not only in the nuclear genome ( 18, 19 ), but also in the mitochondrial genome. Considering that aging is the major risk factor for multiple chronic diseases ( 20, 21 ), our study provides new grounds for further investigation into mitochondrial-encoded regulators of healthy lifespan.