Scope Application of metabolomics to nutrition and health research is increasing and while much effort has been invested in understanding factors that influence the metabolomic profile there is relatively little known about the impact of fitness level. This study aimed to examine the relationship between fitness level, substrate oxidation rates, and the metabolic profile. Methods and results Two hundred and fourteen healthy adults (18–60 years) were recruited and 65 subjects were selected based on their estimated maximal oxygen consumption levels. Metabolomic analysis was performed. The subjects were split into fitness groups according to their maximal oxygen consumption levels (mL/kg/min) and analysis revealed significant differences in normalized fat and carbohydrate oxidation levels between the groups. Urinary metabolomic analysis revealed significantly different profiles in the groups with 15 amino acids significantly higher in the low fitness groups. Effects of fitness level in the plasma metabolic profiles were also demonstrated. Conclusion This study demonstrates a relationship between fitness level and the amino acid profile. Moreover, the metabolite changes show that a reduced excretion of amino acids in adults is associated with increased fitness levels and an increased fat oxidation rate during exercise. Interestingly, higher levels of branched chain amino acids were associated with lower fitness levels and higher insulin resistance.