Context: Type 2 diabetes and cardiovascular disease occur more frequently and at a younger age in South-Asians than Europeans. This may be related to differences in regulation of the fatty acid metabolism during aging. We compared age-related acylcarnitine and amino acid concentrations in Dutch and South-Asian Surinamese study participants. Methods: We measured types of acylcarnitine and amino acid concentrations in plasma (by tandem mass spectrometry) in a random subsample of 350 Dutch and 350 South-Asian Surinamese origin participants of the Healthy Life in an Urban Setting study (Amsterdam, Netherlands). We derived principal components (PCs) from the metabolites. Linear regression was used to assess differences in PCs and individual metabolite concentrations, and their age trends between the groups by sex. We adjusted for body mass index and intake of fat and total energy. Results: Mean age was 44.8 (SD, 13.3) years. Amino acid concentrations were higher among South-Asian Surinamese women compared with Dutch women; acylcarnitine and amino acid levels were higher among South-Asian Surinamese men than Dutch men. Metabolite levels increased similarly with age in both ethnic groups. Results remained similar after adjustment. Conclusion: Ethnic differences in metabolite concentrations suggest that fatty acid and amino acid metabolism are more dysregulated among South-Asian Surinamese compared with Dutch from a young age. During adulthood, metabolites increase similarly in both ethnic groups.