The promotion of healthy energy balance-related behaviours (EBRB) is already important for children at a young age. Different settings, for example childcare and home, play an important role in the EBRB of young children. Further, factors in different types of environment (e.g., physical, sociocultural and political) influence their behaviours. SuperFIT (Systems of Underprivileged Preschoolers in their home and preschool EnviRonment: Family Intervention Trial) is a comprehensive, integrated intervention approach for 2–4 year old children. This paper describes the development and design of the evaluation of SuperFIT. The SuperFIT intervention approach consists of preschool-based, family-based, and community-based components. Intervention activities aimed at changing the physical, sociocultural and political environments in each setting and establishing an increased alignment between the settings. A quasi-experimental design was adopted with twelve intervention and nine control preschools to evaluate effectiveness. The primary outcomes were Body Mass Index (BMI) z-scores (objectively assessed height and weight), dietary intake (24 h recall), and physical activity (accelerometer) of the children. Further, the effects on the nutrition- and physical activity-related practices of preschool teachers and parents were evaluated (questionnaires). Intervention effectiveness was evaluated using linear mixed models. Process evaluation was performed using mixed methods; both quantitative (questionnaires) and qualitative (observations and in-depth interviews) measures were used. The comprehensive, integrated approach of SuperFIT is expected to support healthy EBRB in young children.