The interest in a healthy diet and lifestyle during the early stages of life increased, pointing out its role in the development of noncommunicable chronic diseases throughout adult life. Dietary habits and dietary patterns begin to be established in early childhood and persist during adulthood. Therefore, the EsNuPI (“Nutritional Study in Spanish Pediatric Population”) study aims to depict the dietary patterns, physical activity, and sedentary behaviors in Spanish children aged from one to <10 years old. This prospective, cross-sectional, observational study recruited a total of 1514 children from Spanish cities with >50,000 inhabitants, stratified by Nielsen areas. Participants were involved in one face-to-face survey, followed by a telephone survey after at least one week. Information about dietary intake and habits was obtained using a quantitative food frequency questionnaire and two 24-h dietary recalls. Physical activity and sedentary behaviors were registered using a specific questionnaire based on a seven-day record. Data were processed and stratified by categorical variables to be statistically analyzed in order to meet the study objectives. This study is the first of its kind in a Spanish reference population of this age range and the first to evaluate whether the consumption of adapted milk formulas and dairy products is associated with healthier dietary patterns and better diet quality and lifestyles in this group.