Mitochondrial dysfunction caused by mitochondrial DNA (mtDNA) damage has been associated with the progressive decline of multiple tissues during aging. Muscle satellite cells (MuSCs), which sustain skeletal muscle regeneration throughout life, exhibit reduced number and regenerative capacity with age. Yet, the contribution of mtDNA mutations to MuSC integrity and their impact on skeletal muscle remain poorly understood. Here, we used a dominant-negative variant of the mitochondrial helicase Twinkle (K320E) to induce mtDNA alterations in C2C12 myoblasts and MuSCs and investigated myogenic differentiation. During C2C12 differentiation, impaired mtDNA integrity disrupted respiratory complex assembly, increased reactive oxygen species, and directly compromised proper differentiation. Proximity proteomics in C2C12 differentiated cells revealed that K320E expression not only affects mtDNA encoded proteins, but also reshapes the complete mitochondrial proteome. In vivo, using the fluorescent reporter mitoTIMER, we found that mtDNA alterations in MuSCs, increased mitochondrial oxidation at early stages of differentiation, which normalized at later stages. Finally, by mimicking the age-dependent accumulation of mtDNA alterations, we show that mtDNA defects in MuSCs are transmitted to mature skeletal muscle. These defects induced architectural changes in muscle, including a glycolytic-to-oxidative fiber type transition reminiscent of aging human muscle. Together, our results establish a mechanistic link between mtDNA instability in muscle progenitors and aging of the skeletal muscle. With these results, we demonstrate that alterations in the mtDNA of muscle progenitors are sufficient to drive long-term changes in muscle architecture that may contribute to age-dependent functional decline.