The relationship between physical endurance performance and microbiota composition is of increasing interest as new evidence points to the importance of intestinal flora as a major determinant of athlete health. The full extent of changes that occur in the microbiota during exercise has not yet been studied. To enhance performance and reduce exercise-induced stress, training programs, combined with individualized diets, aim to balance systemic stressors. Nutrients, especially under conditions of stress, have significant and complete effects on energy metabolism, protein synthesis, and the functioning of the endocrine, nervous, and immune systems. The degree to which nutrients regulate the stress response depends on the duration of the stressor, intensity and type of exertion, the physiologic status of the athlete, and the composition and function of the microbiota. Standard dietary plans are difficult to define because of the individual complexity of the stress response in athletes, ranging from digestive problems to catabolic states and depression. Traditionally, athletes are advised to consume high amounts of simple carbohydrates and proteins and limit fat and fiber intake to provide a quick source of energy and avoid digestive problems associated with high fiber intake. Athletes’ diets are based on the use of foods containing micronutrients such as iron, calcium, amino acids, essential fatty acids, and antioxidants, but the effects of these components on the composition of the intestinal microbiota are poorly understood. Controlled regulation of the microbiota through diet may improve performance during training and competition, reduce stress response, and aid in more efficient recovery of body resources.