<p>This study aimed to analyze sex-specific changes in blood pressure (BP), anthropometric variables, and movement behaviors following a 16-week educational intervention of the BeE-school project. This intervention study included 735 children aged 6–10 years from 10 primary schools in the Northern region of Portugal. Schools were randomly assigned to either an intervention group (<i>n</i> = 353) or a control group (<i>n</i> = 382). The intervention consisted of a 16-week teacher education and training program, based on health promotion and its implementation in the classroom. Twice a month, challenges were sent to families during this period. Trained researchers evaluated body mass, height, waist circumference (WC), systolic BP (SBP), diastolic BP (DBP), screen time, sedentary behavior (SB) and physical activity before and after 16 weeks. Body mass index (BMI), tri-ponderal mass index (TMI), and age at peak height velocity were calculated. Data were analyzed using the Mann-Whitney tests, repeated measures ANOVA with Bonferroni post hoc, and Friedman ANOVA for nonparametric variables, with significance set at <i>p</i> ≤ 0.05. After the intervention, girls in the intervention group showed a significant reduction in TMI, while girls in the control group showed an increase in BMI (<i>p</i> &lt; 0.01). Reductions in SBP were observed in both groups, whereas DBP decreased mainly in the intervention group (<i>p</i> &lt; 0.01). In addition, the intervention group showed reduced SB and increased physical activity levels (<i>p</i> &lt; 0.05). The BeE-school intervention was associated with favorable changes in BP, SB, physical activity, and indicators of body adiposity, particularly among girls, supporting the potential benefits of multicomponent school-based health promotion strategies for children from socioeconomically vulnerable contexts.</p><p><b>Clinical trial registration:</b> The study was registered in Clinical Trials database/platform (NCT05395364).</p>