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Using a novel technique of high-density surface EMG decomposition and motor unit (MU) tracking, we compared changes in the properties of vastus medialis and vastus lateralis MU after endurance (END) and high-intensity interval training (HIIT).Sixteen men were assigned to the END or the HIIT group (n = 8 each) and performed six training sessions for 14 d. Each session consisted of 8–12 × 60-s intervals at 100% peak power output separated by 75 s of recovery (HIIT) or 90–120 min continuous cycling at ~65% V˙O2peak (END). Pre- and postintervention, participants performed 1) incremental cycling to determine V˙O2peak and peak power output and 2) maximal, submaximal (10%, 30%, 50%, and 70% maximum voluntary contraction [MVC]), and sustained (until task failure at 30% MVC) isometric knee extensions while high-density surface EMG signals were recorded from the vastus medialis and vastus lateralis. EMG signals were decomposed (submaximal contractions) into individual MU by convolutive blind source separation. Finally, MU were tracked across sessions by semiblind source separation.After training, END and HIIT improved V˙O2peak similarly (by 5.0% and 6.7%, respectively). The HIIT group showed enhanced maximal knee extension torque by ~7% (P = 0.02) and was accompanied by an increase in discharge rate for high-threshold MU (≥50% knee extension MVC) (P < 0.05). By contrast, the END group increased their time to task failure by ~17% but showed no change in MU discharge rates (P > 0.05).HIIT and END induce different adjustments in MU discharge rate despite similar improvements in cardiopulmonary fitness. Moreover, the changes induced by HIIT are specific for high-threshold MU. For the first time, we show that HIIT and END induce specific neuromuscular adaptations, possibly related to differences in exercise load intensity and training volume.