•Mitochondrial dysfunction occurred in two different pork muscles during aging.•Cytochrome c was released and caspase-3 was activated in both muscle types.•PM exhibited higher apoptotic potential compared to LD.•PM showed lower myofibrillar proteolysis than LD.•Apoptosis-mediated proteolysis could be muscle-specific. This study aims to investigate the changes in mitochondrial apoptotic factors and proteolysis of two porcine muscles (psoas major – PM and longissimus dorsi – LD) during aging. Results found that during 2–168 h postmortem mitochondrial membrane permeability, mitochondrial lipid peroxidation, Ca2+ levels were increased, while the reduction level and abundance of cytochrome c were decreased (P < 0.05) in both muscle types. Furthermore, the activation of caspase-3 along with increases in troponin-T and desmin degradation, and μ-calpain autolysis were found (P < 0.05), regardless of muscle type. PM maintained higher mitochondrial apoptotic factors, but had more intact desmin, less troponin-T degradation and less extent of autolyzed products of μ-calpain compared to LD (P < 0.05). These results indicate that the rapid onset of mitochondrial apoptosis of PM would not lead to a subsequent impact on myofibrillar protein degradation, suggesting that the mitochondrial apoptosis mediated tenderization process could be muscle-specific.