Objective: To determine the association between foods habits with mental health (i.e., anxiety, depression, and stress) and executive function (i.e., attention, inhibition, working memory, and cognitive flexibility) in Chilean children and adolescents. Methods: A cross-sectional study with 498 children and adolescents (52.6% female) aged 10–17 years participated. The Krece Plus questionnaire (Food habits), Depression Anxiety Stress Scales (DASS-21, metal health), and the CogniFit (executive functions) test were used to assess the study variables. Results: The poor and moderate food habits groups reported higher prevalence of extremely severe anxiety (poor, 40.8%; moderate, 41.4%; good, 21.6%; p = 0.013) and extremely severe depression (poor, 20.4%; moderate, 21.3%; good, 5.7%; p < 0.001). The food habits were linked inversely to anxiety (β −0.07, 95%CI −0.11 to −0.03, p = 0.001), depression (β −0.08, 95%CI −0.12 to −0.04, p < 0.001), stress (β −0.07, 95%CI −0.11 to −0.02, p = 0.004), and total score of negative mental health (β −0.03, 95%CI −0.04 to −0.01, p < 0.001). Conclusions: The food habits were inversely associated with negative metal health in Chilean children and adolescents, where the good food habits group reported better mental health in all dimensions.