Background <p>Childhood and adolescence are crucial periods for brain development, during which multiple environmental factors, including gut microbiota and dietary habits, play important roles. However, the combined impact of those factors on neurodevelopment and mental disease risk remains largely unexplored. Here, we aimed to investigate the relationships between gut microbiota and diet and their role in classifying behavioral problems that may precede mental disorders in children and adolescents.</p> Methods <p>We performed a cross-sectional study, including data from 335 subjects, including 202 children (5–10&#xa0;years) and 133 adolescents (11–17&#xa0;years). Gut microbiota was analysed in stools by shotgun metagenomics. Dietary habits, lifestyle factors and emotional and behavioral difficulties were screened using validated questionnaires. Penalized Logistic Regression models were trained to classify individuals into Healthy and Behavioral Problem groups based on microbial diversity, differential abundance of bacterial species, dietary patterns, and food and nutrient intakes. Mediation analyses were applied to assess whether gut microbiota mediates the effect of diet on behavioral problems.</p> Results <p>A Western diet characterized by poor adherence to dietary recommendations was consistently associated with behavioral problems in all age groups. Individuals with behavioral problems exhibited distinct gut microbiota profiles characterized by lower levels of short-chain fatty acid-producing bacteria (particularly butyrate-producing species) and higher levels of potential pathogens (e.g., <i>Campylobacter coli</i> and <i>Lautropia mirabilis</i>), linked to poor dietary choices. Furthermore, we evidenced the mediation role of the gut microbiota in the association between dietary patterns and food groups and behavioral problems. In adolescents, <i>L. mirabilis</i> was identified as a mediator of the relationship between a Western diet and behavioral problems, while <i>Anaerostipes rhamnosivorans</i> mediated the relationship between fish consumption and behavioral problems. Gut microbiota data enhanced the classification accuracy of logistic regression models for identifying individuals with behavioral problems over models based solely on dietary data.</p> Conclusion <p>Integrating dietary habits and gut microbiota data enables more accurate stratification of children and adolescents at risk for behavioral problems. Our findings may help to refine dietary interventions targeting the gut microbiota to improve mental health outcomes in these vulnerable populations.</p>