Childhood obesity is one of the main public health concerns in Europe. The aim was to identify possible risk factors associated with overweight/obesity in Spanish preschool and school-age children. The sample (1075 (50.7% girls) children aged 3 to 12) is part of the project ‘Alimentando el Cambio’ whose objective is to promote healthy lifestyles in schools. Child height and weight were measured, and parents filled out questionnaires related to the children’s lifestyle. There was a positive and significant association between sweetened beverage consumption and body mass index (BMI) z-score in both sexes and age groups. There was a negative and significant association between BMI z-score and dairy products in girls of both age groups. There was also a protective effect of regular nut consumption on overweight/obesity in girls 6–12 y. Night-time sleep during weekdays showed a negative association with BMI z-score for older boys and girls. A positive and significant association was found between total screen time and BMI z-score during weekdays. Regarding emotional well-being and self-esteem, having girls 6–12 y laughing and feeling happy and good about themselves in the last week was a protective factor against overweight/obesity. Childhood obesity prevention efforts may benefit from targeting these key risk factors.