This study aimed to investigate and compare the effects of repeated-sprint (RSH) and sprint interval training in hypoxia (SIH) on sea level running and cycling performance, and to elucidate potential common or divergent adaptations of muscle perfusion and -oxygenation as well as mitochondrial respiration of blood cells. Eleven team-sport athletes performed either RSH (3x5x10s, 20s and 5min recovery between repetitions and sets) or SIH (4x30s, 5min recovery) cycling training for 3weeks (3 times/week) at a simulated altitude of 2,200m. Before and three days after the training period, a Wingate and a repeated cycling sprint test (5x6s, 20s recovery) were performed with a 30min resting period between the tests. Four to five days after the training, participants performed a repeated running sprint test (RSA, 6x17m back and forth, 20s recovery) and a Yo-Yo intermittent recovery test (YYIR2) with 1 hour active recovery between tests. The order of the tests as well as the duration of the resting periods remained the same before and after the training period. During the cycling tests near-infrared spectroscopy was performed on the vastus lateralis. In four participants, mitochondrial respiration of peripheral blood mononuclear cells (PBMC) and platelets was measured before and after training. YYIR2 running distance increased by +96.7 ± 145.6 m after RSH and by +100.0 ± 51.6 m after SIH (p = 0.034, eta² = 0.449). RSA mean running time improved by -0.138 ± 0.14s and -0.107 ± 0.08s after RSH and SIH respectively (p = 0.012, eta² = 0.564). RSH compared to SIH improved re-oxygenation during repeated sprinting. Improvements in repeated cycling were associated with improvements in re-oxygenation (r = 0.707, p <0.05). Mitochondrial electron transfer capacity normalized per PBMC count was decreased in RSH only. This study showed that cycling RSH and SIH training improves sea-level running performance. Our preliminary results suggest that RSH and SIH training results in different patterns of muscular oxygen extraction and PBMC mitochondrial respiration, without effect on platelets respiration.