School-based health promotion interventions have been shown to lead to measurable changes in the nutrition and physical activity behaviors. This study examines whether the impact of an intervention program on students’ healthy eating and physical activity was mediated by teacher training and engagement in health promotion. The trial was conducted in three phases: needs assessment of the baseline survey of teachers, mothers’ and children; intervention among seven randomly selected schools that included teacher training in healthy eating and physical activity; and a post-intervention evaluation survey. The SPSS PROCESS for Hayes (Model8) was used to determine moderation and mediation effects. The difference in difference (DID) was calculated for the three main outcomes of the study: eating breakfast daily (DID = 17.5%, p < 0.001); consuming the recommended servings of F&V (DID = 29.4%, p < 0.001); and being physically active for at least 5 days/week (DID = 45.2%, p < 0.001). Schoolchildren’s eating breakfast daily was mediated by their teachers’ training in nutrition (β = 0.424, p = 0.002), teachers’ engagement (β = 0.167, p = 0.036), and mothers preparing breakfast (β = 1.309, p < 0.001). Schoolchildren’s consumption of F&V was mediated by teachers’ engagement (β = 0.427, p = 0.001) and knowing the recommended F&V servings (β = 0.485, p < 0.001). Schoolchildren’s physical activity was mediated by their teachers’ training in physical activity (β = 0.420, p = 0.020) and teachers’ engagement (β = 0.655, p < 0.001). Health behavior changes in the school setting including improvements in eating breakfast, consuming the recommended F&V and physical activity was mediated by teacher training and engagement. Effective teacher training leading to teacher engagement is warranted in the design of health-promotion interventions in the school setting.