Childhood obesity prevention is a leading public health challenge requiring the adoption of healthy lifestyles at an early age. We examined how the kindergarten environment can promote eating sensibly, drinking water and becoming physically active. The effects of an intervention program among 42 Israeli kindergartens (1048 children, aged 4–6) whose teachers participated in a health education training program were compared to 32 kindergartens (842 children) whose teachers did not undergo this training program. An eight-month intervention program focused on knowledge/mathematical/logical/critical thinking, self-regulation/control acquisition, and sensible decision-making abilities. We hypothesized that nutrition and physical-exercise-oriented intervention programs, combining knowledge/mathematical logical thinking, would positively impact the quality of children’s mid-morning snack and water consumption, their ability to express feelings following physical exercise, and the adoption of healthy lifestyles at home. The quality of mid-morning snacks and water consumption were observed in both groups pre- and post-intervention. Qualitative interviews documented children’s subjective feelings following physical exercise. A significant improvement (p< 0.001) was observed in the mid-morning snacks composition and in water drinking habits in the intervention group; 80% of children offered a physiological explanation regarding energy expenditure processes following intense physical exercise. In conclusion, kindergarten interventions implemented by trained teachers can promote adoption of health behaviors necessary for obesity prevention.