Background: Schools can play an important role in promoting children`s health behaviours. A Dutch initiative, `The Healthy Primary School of the Future`, aims to integrate health and well-being into the school system. We use a contextual action-oriented research approach (CARA) to study the implementation process. Properties of CARA are its focus on contextual differences and the use of monitoring and feedback to support and evaluate the process of change. The aim of this article is to describe the use of the approach. Methods: Four schools (each with 200-300 children, aged 4-12 years) were included; all located in low socio-economic status areas in the south of the Netherlands. Data collection methods include interviews, observations, questionnaires, and health and behavioural measurements. Research contributions include giving feedback and providing schools with a range of possibilities for additional changes. The contextual data we examine include schools` health promoting elements, practices of teachers and parents, dominating organisational issues, and characteristics of the student population; process data include the presence of potential barriers to changes. Discussion: CARA is an adaptive research approach that generates knowledge and experiences on how to deal with health promotion in complex systems. We think this approach can set an example for research efforts in comparable initiatives.