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Urinary metabolic profiling is a promising powerful tool to reflect dietary intake and can help understand metabolic alterations in response to diet quality. Here, we used 1H NMR spectroscopy in a multicountry study in European children (1147 children from 6 different cohorts) and identified a common panel of 4 urinary metabolites (hippurate, N-methylnicotinic acid, urea, and sucrose) that was predictive of Mediterranean diet adherence (KIDMED) and ultra-processed food consumption and also had higher capacity in discriminating children's diet quality than that of established sociodemographic determinants. Further, we showed that the identified metabolite panel also reflected the associations of these diet quality indicators with C-peptide, a stable and accurate marker of insulin resistance and future risk of metabolic disease. This methodology enables objective assessment of dietary patterns in European child populations, complementary to traditional questionary methods, and can be used in future studies to evaluate diet quality. Moreover, this knowledge can provide mechanistic evidence of common biological pathways that characterize healthy and unhealthy dietary patterns, and diet-related molecular alterations that could associate to metabolic disease. The HELIX project has received funding from the European Community’s Seventh Framework Programme (FP7/2007–2013) under grant agreement no. 308,333. The STOP project (http://www.stopchildobesity.eu/) received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement no. 774,548. The STOP Consortium is coordinated by Imperial College London and includes 24 organizations across Europe, the United States, and New Zealand. The content of this publication reflects only the views of the authors, and the European Commission is not liable for any use that may be made of the information it contains. INMA data collections were supported by grants from the Instituto de Salud Carlos III, CIBERESP, and the Generalitat de Catalunya-CIRIT. KANC was funded by the grant of the Lithuanian Agency for Science Innovation and Technology (6-04-2014_31 V-66). For a full list of funding that supported the EDEN cohort, refer to: Heude B et al. Cohort Profile: The EDEN mother–child cohort on the prenatal and early postnatal determinants of child health and development. Int J Epidemiol. 2016 Apr;45(2):353–63. The Norwegian Mother, Father and Child Cohort Study (MoBa) is supported by the Norwegian Ministry of Health and Care Services and the Ministry of Education and Research. The Rhea project was financially supported by European projects, and the Greek Ministry of Health (Program of Prevention of Obesity and Neurodevelopmental Disorders in Preschool Children, in Heraklion district, Crete, Greece: 2011–2014; 'Rhea Plus': Primary Prevention Program of Environmental Risk Factors for Reproductive Health, and Child Health: 2012–2015). Born in Bradford received funding from the Wellcome Trust (101597). Professor Wright and McEachan receive funding from the National Institute for Health Research Applied Research Collaboration for Yorkshire and Humber. The views expressed are those of the author(s) and not necessarily those of the NIHR or the Department of Health and Social Care. Dr. Maribel Casas received funding from Instituto de Salud Carlos III (Ministry of Economy and Competitiveness) (MS16/00128). Dr. Leda Chatzi was supported by NIH/NIEHS R01 ES029944, R01ES030691, R01ES030364, R21 ES029681, R21 ES028903, and P30 ES007048-23. Dr. David Conti was supported by P01CA196569, R01CA140561, R01 ES016813, R01 ES029944, R01ES030691, and R01ES030364. Dr. Nikos Stratakis was supported by NIH/NIEHS R21 ES029681 and P30 ES007048-23, and NIH/NIDDK P30 DK048522-24. Dr. Hector Keun and Dr. Alexandros Siskos were also supported by the European Union’s Horizon 2020 research and innovation programme under grant agreement no. 874,583 ('ATHLETE'). Dr. Eleni Papadopoulou was supported by the Research Council of Norway, under the MILJØFORSK program (project no. 268465). Dr. Fernanda Rauber was supported by the Fundação de Amparo à Pesquisa do Estado de São Paulo 2016/14302-7 and 2018/19820-1. The CRG/UPF Proteomics Unit is part of the Spanish Infrastructure for Omics Technologies (ICTS OmicsTech) and it is a member of the ProteoRed PRB3 consortium which is supported by grant PT17/0019 of the PE I + D + i 2013–2016 from the Instituto de Salud Carlos III (ISCIII) and ERDF. ISGlobal acknowledges support from the Spanish Ministry of Science, Innovation and Universities, 'Centro de Excelencia Severo Ochoa 2013–2017', SEV-2012–0208, and 'Secretaria d’Universitats i Recerca del Departament d’Economia i Coneixement de la Generalitat de Catalunya' (2017SGR595).