Objective: 31P magnetic resonance spectroscopy (MRS) was used to document long lasting losses in muscle oxidative capacity after bouts of intense endurance exercise. Methods: The subject was a 34 year old highly fit female cyclist (Vo2MAX = 53.3 ml/kg/min). Over a five month period, she participated in three separate intense bouts of acute unaccustomed exercise. 31P MRS measurements were performed seven weeks after the first bout and every two weeks for 14 more weeks. In all cases, 31P MRS measurements followed three days after each bout. Results: The subject showed a decreased ability to generate ATP from oxidative phosphorylation and an increased reliance on anaerobic ATP production during the 70% and 100% maximal voluntary contractions after the exercise bouts. Increased rates of fatigue and increased indicators of exercise difficulty also accompanied these reductions in muscle oxidative capacity. Increased oxidative and anaerobic ATP production were needed to maintain the work level during a submaximal 45% maximal voluntary contraction exercise. Conclusions: Acute increases in intensity accompanied by a change in exercise mode can influence the ability of muscle to generate ATP. The muscles were less economical and required more ATP to generate force during the submaximal exercises. During the maximal exercises, the muscle's mitochodria showed a reduced oxidative capacity. However, these reductions in oxidative capacity at the muscle level were not associated with changes in whole body maximal oxygen uptake. Finally, these reductions in muscular oxidative capacity were accompanied by increased rates of anaerobic ATP production, fatigue, and indicators of exercise difficulty.