Abstract Background The onset of inadequate behaviors leading to the development of risk factors for chronic diseases is known to occur early in life. An effective program for health promotion should therefore focus on children and their environment, as the starting point for behavior development. The overarching objective of the Program SI! (Salud Integral - Comprehensive Health) is to intervene at the school level, to establish and develop life-lasting habits that will help preserving health during adulthood. The Program SI! comprises five consecutive subprograms according to the five stages of education in Spain, the first being in preschoolers. This study aims to evaluate the efficacy of Program SI! to establish and improve lifestyle behaviors in children (preschoolers aged 3–5 years), their parents, and teachers, and also improving the school environment. A secondary objective is to evaluate improvements in cardiovascular health-related markers (anthropometric parameters, blood pressure, and dietary and physical activity patterns) in these same children. Methods/design 24 public schools from the city of Madrid (Spain) were allocated through stratified randomization to intervention or control. The intervention schools follow the Program SI!, which provides didactic units, emotions cards, healthy tips, and online resources. The intervention schools integrate the Program SI! into their scholar curriculum organized in four complete weeks during each academic year during the 3 years of preschool education. Control schools follow their normal curriculum. Primary outcomes are 1-year, and 3-year changes from baseline of scores for knowledge, attitudes, and habits (KAH) of children, their parents and teachers in regards to a healthy lifestyle. Secondary outcomes are 1-year, and 3-year changes from baseline in clinical and anthropometric parameters of children. Discussion The Program SI! is a long-term health promotion program starting in 3 years old. It incorporates the traditional areas of intervention (diet and physical activity), introducing additional components such as knowledge of the human body and management of emotions to achieve a comprehensive intervention. The Program SI! is designed to be an effective, sustainable health promotion program for the adoption of healthy behaviors from early in life. Trial registration Trial registration number: NCT01579708