<p>To improve performance at altitude some endurance athletes undergo exposure to hypoxic stimulus during post exercise recovery, but this may impact gene expression related to exercise adaptation. The purpose of this study is to determine a hypoxic threshold and its impact on gene expression related to oxygen sensing, metabolism, and mitochondrial dynamics. Ten male participants (24 ± 4 years, 47.1 ± 9.5&#xa0;ml·kg^− 1·min^− 1 ) completed 4 trials at least 7 days apart. Each trial consisted of cycling for one hour at 70% of Wpeak in normoxia before recovering for 6&#xa0;h in a simulated environment [0&#xa0;m, 1,667&#xa0;m, 3,333&#xa0;m, and 5,000&#xa0;m]. Muscle samples were collected from the <i>vastus lateralis</i> before exercise and after recovery. Pulse oxygen saturation (SPO₂) was measured before exercise, during exercise, and during recovery. SPO₂ lowered with increasing elevation (<i>p</i> &lt; 0.001 for all trials). Gene expression of PGC-1α, HIF-1α, and HK increased following recovery from exercise (<i>p</i> = 0.048, <i>p</i> = 0.013, and <i>p</i> = 0.014), but there were no differences between trials (<i>p</i> &gt; 0.05). No differences were observed for HIF-2α, PFK, FIS, MFN 2, and OPA (<i>p</i> &gt; 0.05). Post aerobic exercise recovery at graded levels of simulated hypoxia does not affect the expression of genes related to oxygen sensing, metabolism, and mitochondrial dynamics, compared to normoxia.</p>