The global rate of obesity in childhood is becoming an epidemic and many authors have established a significant association between childhood obesity and overweight in adulthood. It is therefore necessary to seek effective strategies to reduce these levels of obesity. The aim of this study was to evaluate the impact of the Healthy Habits Program (HHP). The participants comprised 158 children from the fifth and sixth grades (intervention group, n = 82; control group, n = 76). The HHP is a school-based physical activity program focusing on promoting a healthy lifestyle. It lasted for 8 months, and measurements were taken at the beginning and end of the program. Physiological variables (total cholesterol, triglycerides, blood glucose, blood pressure, and maximal oxygen consumption), anthropometric variables (body mass index (BMI)) and behavioral variables (breakfast, quality of diet, meal frequency, physical activity, sedentary behavior, sleep, and perceived health) were evaluated. Repeated-measures ANOVA showed significant improvements (p < 0.05) after the intervention for the intervention group in triglycerides, blood glucose and maximal oxygen consumption. Significant improvements were also observed in breakfast habits and quality of diet. Finally, a significant improvement in prevalence of normal levels was observed for total cholesterol, blood pressure, and BMI. It can therefore be stated that the HHP is an innovative and useful school-based program that can help to improve diet and health in childhood.