It has not been established which physiological processes contribute to endurance training-related changes () in aerobic performance. For example, the relationship between intramuscular metabolic responses at the intensity used during training and improved human functional capacity has not been examined in a longitudinal study. In the present study we hypothesized that improvements in aerobic capacity (VO₂max) and metabolic control would combine equally to explain enhanced aerobic performance. Twenty-four sedentary males (23±1 y; 1.82±0.02 m; 78.6±2.7 kg) undertook supervised cycling training (45 min at 70% of pre-training (VO₂max) 4 times per week for 6 weeks. Performance was determined using a 15-min cycling time trial, and muscle biopsies were taken before and after a 10-min cycle at 70% of pre-training (VO₂max to quantify substrate metabolism. Substantial inter-individual variability in training-induced adaptations was observed for most parameters, yet 'low responders' for VO₂max were not consistently low responders for other variables. While VO₂max and time trial performance were related at baseline (R2=0.80, p<0.001), the change in VO₂max was completely unrelated to the change in aerobic performance. The maximal parameters VEmax and Veqmax (VE/VO₂max) accounted for 64% of the variance in VO₂max (p<0.001), whereas performance was related to changes in the submaximal parameters Veqsubmax (R²=0.33; p<0.01), muscle lactate (R²=0.32; p<0.01) and acetyl-carnitine (R²=0.29; p<0.05). This study demonstrates that improvements in high intensity aerobic performance in humans are not related to altered maximal oxygen transport capacity. Altered muscle metabolism may provide the link between training stimulus and improved performance, but metabolic parameters do not change in a manner which relates to aerobic capacity changes.