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Diet is one of the most important modifiable lifestyle factors for preventing and treating obesity. In this respect, the Mediterranean diet (MD) has proven to be a rich source of a myriad of micronutrients with positive repercussions on human health. Herein, we studied an observational cohort of children and adolescents with obesity (N = 26) to explore the association between circulating blood trace elements and the degree of MD adherence, as assessed through the KIDMED questionnaire. Participants with higher MD adherence showed better glycemic/insulinemic control and a healthier lipid profile, as well as raised plasma levels of selenium, zinc, cobalt, molybdenum, and arsenic, and increased erythroid content of selenium. Interestingly, we found that these MD-related mineral alterations were closely correlated with the characteristic metabolic complications behind childhood obesity, namely hyperglycemia, hyperinsulinemia, and dyslipidemia (p < 0.05, |r| > 0.35). These findings highlight the pivotal role that dietary trace elements may play in the pathogenesis of obesity and related disorders.