A fundamental issue in the metabolic field is whether it is possible to understand underlying mechanisms that characterize individual variation. Whole-animal performance relies on mitochondrial function as it produces energy for cellular processes. However, individual variation in mitochondrial traits lack of longitudinal measures to evaluate how mitochondrial function can change within and among individuals and with environmental context. The aims of this study were to test the repeatability of muscle mitochondrial metabolism thanks to two biopsies performed in red muscle, and to evaluate effects of biopsies on whole-animal performance in goldfish Carassius auratus. Our results show that basal mitochondrial respiration and net phosphorylation efficiency are repeatable at 14-day intervals. We also show that swimming performance (optimal cost of transport and critical swimming speed) was repeatable in biopsied fish, whereas the repeatability of individual oxygen consumption (standard and maximal metabolic rates) seemed not stable over time. However, we noted that the means of individual and mitochondrial traits did not change over time in biopsied fish. This study shows that muscle biopsies allow the measurements of mitochondrial metabolism without