Top-level performances in endurance sports require several years of hard training loads. A major objective of this endurance training is to reach the most elevated metabolic adaptations the athlete will be able to support. As a consequence, overtraining is a recurrent problem that highly-trained athletes may experience during their career. Many studies have revealed that overtraining could be highlighted by various biochemical markers but a principal discrepancy in the diagnosis of overtraining stems from the fact that none of these markers may be considered as universal. In endurance sports, the metabolic aspects of training fatigue appear to be the most relevant parameters that may characterise overtraining when recovery is not sufficient, or when dietary habits do not allow an optimal replenishment of substrate stores. From the skeletal muscle functions to the overall energetic substrate availability during exercise, six metabolic schemes have been studied in relation to overtraining, each one related to a central parameter, i.e. carbohydrates, branched-chain amino acids, glutamine, polyunsaturated fatty acids, leptin, and proteins. We summarise the current knowledge on these metabolic hypotheses regarding the occurrence of overtraining in endurance sports.