Purpose This study investigated the change in mitochondrial capacity and VO2max in elite triathlon, cycling, and Greco-Roman wrestling athletes over a 28-day training period. Methods Sixteen elite athletes (23 ± 2.5 years; 176 ± 6 cm; 76 ± 8 kg; 65 ± 6.9 ml/min/kg) participated. Mitochondrial capacity was assessed before (pre) and after (post) a 28-day training period by measuring the increase in deoxygenated hemoglobin (HHb) in the m. vastus lateralis during three consecutive one-minute rapid cuff occlusion periods using near-infrared spectroscopy. VO2max was measured via a treadmill ramp test at the same time points. Results The analyses revealed significant differences between pre- and post-measurements, with significant improvements in the second (Δτ2 = − 3.4 ± 2.7 s, p = 0.001) and third (Δτ3 = − 5.0 ± 5.1 s, p = 0.006) occlusion period. Correlation analyses demonstrated a moderate negative relationship between the first occlusion tau (τ) rate and VO2max at pre-test (r = − 0.58, p = 0.02) and an even stronger negative correlation at post-test (r = − 0.62, p = 0.01). Within-subject analysis identified 14 athletes as responders. Conclusion The changes in τ rates indicate significant improvements in mitochondrial capacity over a period of 28 days in elite athletes, underscoring the utility of NIRS-derived τ rates for monitoring changes in elite athletes.