Abstract An increasing number of schools obtained a Healthy School certificate, yet little is known about factors, characteristics, and processes, i.e. conditions, influencing the effectiveness of the Healthy School program. Therefore, a mixed methods evaluation study will be conducted on three levels: the student, the school, and the region. The research questions are focused on: 1) conditions for student outcomes, 2) conditions for implementation in schools, and 3) conditions for regional support. For the evaluation, the school and region are considered complex adaptive systems. Conditions for intended outcomes on student lifestyle, health, and academic achievement will be examined using a combination of existing datasets including school codes. Based on student outcomes, best and worst performing schools will be selected for predominantly qualitative analysis to further explain differences. To get insight into conditions for implementation in schools and regional support in nine regions, the degree of implementation will be determined with a questionnaire to select schools for predominantly qualitative analysis. Combined, this study will not only provide insight into the current situation on the three levels, but also explain differences between regions, schools, and students. Consequently, it will be possible to provide concrete advice to strengthen implementation of the Healthy School program.