Identifying the physiological mechanisms underpinning inter-individual differences in performance and fitness remains a key challenge in organismal biology. Variation in mitochondrial aerobic metabolism has been suggested to underlie inter-individual variation in performance, but this remains seldom tested, partly because of the need to use terminal sampling for assessing mitochondrial parameters. To fill this knowledge gap, we investigated whether inter-individual variation in mitochondrial aerobic parameters measured from less-invasively taken samples (i.e., blood cells) would correlate with both anaerobic and aerobic metrics of flight performance in house sparrows (Passer domesticus). We predicted that mitochondrial aerobic metabolism should correlate with aerobic but not anaerobic metrics of flight performance. As expected, we found no evidence for a relationship between mitochondrial metabolism and the energy required to take-off (i.e., anaerobic), but flight duration to exhaustion (i.e., aerobic) correlated positively with both cellular mitochondrial respiration rates and oxidative phosphorylation efficiency, a proxy of mitochondrial efficiency to convert nutrients into ATP. Our results therefore support the idea that inter-individual variation in mitochondrial aerobic metabolism could underlie variation in aerobic performance, and suggest that the nucleated blood cells of birds (and potentially other non-mammalian vertebrates) may be a relevant tissue to test those links.