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Diet plays an essential role in health and disease. Therefore, its determination is an important component of many investigations. The aim of the study was to evaluate the effect of a nutritional intervention on the urinary metabolome in children aged 6–12 years. Also, it was intended to identify biomarkers of diet quality and dietary intake. A 2‐month, randomized, controlled, parallel trial was conducted in Spanish children. The analyses focused on the ALINFA group, which followed a full‐fixed meal plan including healthy products, ready‐to‐eat meals, and healthy recipes. Diet quality was assessed by the KIDMED index and dietary intake by a food frequency questionnaire. Untargeted metabolomic analysis on urine samples was carried out, and multivariate analyses were performed for pattern recognition and characteristic metabolite identification. PLS‐DA and Volcano plot analyses were performed to identify the discriminating metabolites of this group. 12 putative metabolites were found to be the most relevant to this intervention. Most of them were products derived from protein and amino acid metabolism (N‐Ribosylhistidine, indolacrylic acid, and peptides) and lipid metabolism (3‐oxo‐2‐pentylcyclopentane‐1‐hexanoic acid methyl, Suberoyl‐L‐carnitine, and 7‐Dehydrodichapetalin E). All these metabolites decreased after the intervention, which was mainly associated with a decrease in the consumption of fatty meat and total fat, especially saturated fat. In turn, N‐Ribosylhistidine and Suberoyl‐L‐carnitine were negatively associated with diet quality, as well as able to predict the change in KIDMED index. In conclusion, the changes observed in urinary metabolome demonstrate the effectiveness of the ALINFA nutritional intervention. [ABSTRACT FROM AUTHOR]