Purpose: The recovery of muscle oxygen consumption (mV˙ O2) after exercise provides a measure of skeletal muscle mitochondrial capacity, as more and better-functioning mitochondria will be able to restore mV˙ O2 faster to the pre-exercise state. The aim was to measure muscle mitochondrial capacity using near-infrared spectroscopy (NIRS) within a healthy, normally active population and relate this to parameters of aerobic fitness, investigating the applicability and relevance of using NIRS to assess muscle mitochondrial capacity non-invasively. Methods: Mitochondrial capacity was analysed in the gastrocnemius and flexor digitorum superficialis (FDS) muscles of eight relatively high-aerobic fitness (V˙ O2peak ≥ 57 mL/kg/min) and eight relatively low-aerobic fitness male subjects (V˙ O2peak ≤ 47 mL/kg/min). Recovery of whole body V˙ O2, i.e. excess post-exercise oxygen consumption (EPOC) was analysed after a cycling protocol. Results: Mitochondrial capacity, as analysed using NIRS, was significantly higher in high-fitness individuals compared to low-fitness individuals in the gastrocnemius, but not in the FDS (p = 0.0036 and p = 0.20, respectively). Mitochondrial capacity in the gastrocnemius was significantly correlated with V˙ O2peak (R2 = 0.57, p = 0.0019). Whole body V˙ O2 recovery was significantly faster in the high-fitness individuals (p = 0.0048), and correlated significantly with mitochondrial capacity in the gastrocnemius (R2 = 0.34, p = 0.028). Conclusion: NIRS measurements can be used to assess differences in mitochondrial muscle oxygen consumption within a relatively normal, healthy population. Furthermore, mitochondrial capacity correlated with parameters of aerobic fitness (V˙ O2peak and EPOC), emphasising the physiological relevance of the NIRS measurements.