Introduction: Despite the critical function of a nutritionist, only a few sports training centres for students in Indonesia have one. This study aimed to determine the effect of the nutrition care process (NCP) on athletes’ nutritional status and aerobic capacity performance. Methods: This cohort study was conducted in 2022 (May–August) in four training centres (TC) in Indonesia. Subjects were athletes who have been dwelling in TC for at least three months, excluding those absent for >14 days due to a competition or other commitments during the data collection period. NCP included the assistance of trained sports nutritionists. In total, 114 athletes participated in this study: 90 strength athletes and 24 endurance athletes. The participants were aged 14-19 years old with approximately (mean+SD) 6+2.5 years of experience in specific sports. Results: After three months of NCP, knowledge of nutrition (p=0.013), body fat composition (p<0.001), skinfold thickness scores (p<0.001), and performance (p<0.001) of athletes significantly improved. In spite of good intakes of protein and fat, none of the intakes showed significant changes (p>0.05). Furthermore, improved knowledge of sports nutrition and exercise science had a positive impact on dormitory meal choices. Conclusion: Overall, three months of NCP had a significant effect on athletes’ knowledge of nutrition, body fat composition, skinfold thickness, and also VO2Max.