BACKGROUND: In the context of the rapid nutrition transition experienced by middle-income countries of the Arab region, children and adolescent's food choices and dietary behaviors are early risk factors for the development of non-communicable diseases. Assessment of factors influencing food choices among this age group is challenging and is usually based on self-reported data, which are prone to information and recall bias. As the popularity of technologies and video gaming platforms increases, opportunities arise to use these tools to collect data on variables that affect food choice, dietary intake, and associated outcomes. This protocol paper describes the SCALE study (School and community drivers of child diets in Arab cities; identifying levers for intervention) which aims to explore the environments at the level of households, schools and communities in which children's food choices are made and consequently identify barriers and enablers to healthy food choices within these environments. METHODS: Field studies are being conducted in primary schools, among children aged 9-12 years, in Greater Beirut, Lebanon and Greater Tunis, Tunisia. A stratified random sample of 50 primary schools (public and private) are selected and 50 children are randomly selected from grades 4-5-6 in each school. The study includes surveys with children, parents/caregivers, school directors, teachers, and nutrition/health educators to assess individual diets and the contextual factors that influence children's food choices. Innovative locally adapted tools and methods such as game-based choice experiments, wearable cameras and neighborhood mapping are used to describe the environments in which children's food choices are made. DISCUSSION: The SCALE study will generate contextual knowledge on factors in school and neighborhood environments that influence child dietary behaviors and will inform multi-level interventions and policies to address childhood malnutrition (under-and over-nutrition). By integrating methods from various disciplines, including economics, data science, nutrition, and public health and by considering factors at various levels (home, school, and neighborhood), the study will identify levers for intervention with the potential to improve children's dietary behaviors. This will help fill existing gaps in research on food systems and consequently guide positive change in Lebanon and Tunisia, with the potential for replicability in other contexts.