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Prediabetes is a pathological condition in which the blood glucose concentration is higher than normal concentrations but lower than those considered necessary for a type 2 diabetes mellitus diagnosis. Various authors have indicated that the Mediterranean Diet is one of the dietary patterns with the most healthy outcomes, reducing high levels of HbA1c, triglycerides, BMI, and other anthropometric parameters. The main objective of this study was to determine the efficacy of the nutritional intervention for children with prediabetes, including the effectiveness of this nutritional education regarding anthropometric parameters. A randomized pilot trial with two groups, an experimental group (EG) and a control group (CG), using intervention in dietary habits with nutritional reinforcement was carried out on 29 children with prediabetes from a rural area. The nutritional intervention was analyzed through astrophotometric and glycemic measurements and validated surveys. Results: The results indicated improvement in eating habits, adherence to the Mediterranean diet, anthropometric measurements, mainly body mass index and perimeters, and analytical parameters, with a significant decrease in glycated hemoglobin in the EG compared to the CG (p < 0.001). Although the results showed that both groups’ anthropometric parameters improved, a more significant decrease was observed in the experimental group compared to the control.