Amino acid metabolites in biofluids are associated with high body mass index (BMI) and cardiometabolic abnormalities. However, prospective investigations regarding these associations are few, particularly among young individuals. Moreover, little is presently known about the impact of long-term high BMI. Using data from the DOrtmund Nutritional and Anthropometric Longitudinally Designed study (111 males and 107 females), we prospectively investigated relations between repeatedly measured urinary levels of 33 metabolites and (1) previously identified long-term BMI trajectory groups from childhood into late adolescence and (2) cardiometabolic risk markers in late adolescence-young adulthood, in sex-specific linear mixed regression models. Males with long-term overweight had lower indole-3-acetic acid when compared to others. Further, methionine, isoleucine, tryptophan, xanthurenic acid, and indole-3-carboxaldehyde were negatively associated with C-reactive protein (CRP), but 5-hydroxyindole-3-acetic acid was positively associated with CRP. No associations were observed in females. Long-term overweight from childhood into late adolescence is associated with decreased urinary levels of gut bacteria-derived indole-3-acetic acid, and several urinary amino acids, including gut bacteria-derived indole-3-carboxaldehyde are associated with elevated CRP later on in life. taken together, our data suggest that indole metabolites, and their gut bacteria producers play potentially important roles in overweight-related inflammation. High body mass index (BMI) during childhood and adolescence is still a major public health concern 1,2. The condition contributes to the development of cardiometabolic abnormalities such as inflammation over the life course 3. Dysregulated metabolism is one of the biological mechanisms through which high BMI contributes to the development of these cardiometabolic abnormalities 4,5. Scientific efforts have focused on carbohydrate and lipid metabolic perturbations as one of these mechanisms, interest in the impact of unfavorable alterations in protein/amino acid metabolism is now emerging 6,7. Therefore, it would be necessary to explore the link of high BMI, amino acid metabolites, and cardiometabolic abnormalities.