High-level athletic performance requires the implementation of personalized strategies based on the analysis of metabolic pathways involved in energy production: phosphagen, glycolytic, and oxidative pathways. In this context, mitochondria play an essential role as the central regulator of energy production, being closely linked to these three pathways. Exercise boosts cellular respiration, which can also be optimized by nutritional interventions and targeted supplementation, promoting mitochondrial biogenesis, reducing oxidative stress and increasing ATP production. These metabolic adaptations improve athletic performance, accelerate recovery processes, and reduce the risk of injury, adapting to the physiological characteristics of each athlete. Moreover, some of these metabolic adaptations converge on specific targets whose expression or activity is also altered in mental disorders. Therefore, the aim of this review is to analyze mitochondrial adaptations induced by exercise and supplementation, evaluating their impact on the phosphagen, glycolytic, and oxidative metabolic pathways, as well as their relationship with optimizing performance and recovery in high-level athletes, with special attention to their potential application to mental health.