Exercise training in hypoxia enhances physiological adaptations improving exercise performance. However, acute hypoxia generally reduces high-intensity exercise tolerance, limiting its application in sports training. Here, we investigated whether oxygen consumption and exercise tolerance are affected during a session of an emerging high-intensity intermittent training (HIIT) model in hypoxia. This model involves efforts in normoxia with inter-effort hypoxia (IEH) recoveries. Young active males were recruited and completed a graded exercise test in normoxia, followed by HIIT sessions under three conditions: normoxia, continuous normobaric hypoxia (FIO2: ~0.13), and IEH recovery, in different days and random order. Oxygen consumption, ventilatory variables and muscle oxygenation in the vastus laterali were assessed during HIIT sessions consisting of ten 1-min efforts (at 120% of maximal treadmill running speed from the graded test), with 2-min passive recoveries. Compared to normoxia, IEH recovery caused significant hemoglobin desaturation (between 95% and 88%) and a ~ 14% decrease in V̇O2 during recoveries. During efforts, particularly in the first 30 s, VO2 was significantly increased by approximately 7% in the IEH condition compared to normoxia. Notably, exercise task completion was nearly identical between normoxia (87 ± 24%) and IEH recovery conditions (87 ± 18%), but significantly lower in continuous hypoxia (44 ± 27%), along with impaired indexes of O2 metabolism. Additionally, IEH recovery resulted in a significantly lower pulmonary O2 diffusion gradient at a given V̇O2, suggesting a compensatory increase in blood flow. In conclusion, IEH recovery preserved muscle oxygenation and exercise performance while enhancing V̇O2 during efforts.