Introduction In this study, researchers collaborate with children from a low socioeconomic neighbourhood in Amsterdam in developing, implementing and evaluating interventions targeting their health behaviours. This Youth Participatory Action Research project focuses on the promotion of physical activity and healthy dietary behaviour. Methods and analysis This study is a controlled trial using participatory methods to develop interventions together with children aged 9-12 years. At four primary schools in a low socioeconomic neighbourhood in Amsterdam, an 'Action Team' is installed: A group of six to eight children who actively participate as co-researchers in developing, implementing and evaluating interventions. An academic researcher facilitates the participatory process. Four control schools, also located in low socioeconomic areas in and around Amsterdam, continue with their regular curriculum and do not participate in the participatory process. For the effect evaluation, physical activity and sedentary behaviour are assessed using accelerometers and self-reporting; dietary behaviour using self-reporting and motor fitness (strength, flexibility, coordination, speed and endurance) using the motor performance fitness test. Effectiveness of the interventions is evaluated by multilevel regression analysis. The process of co-creating interventions and the implemented interventions is continually evaluated during meetings of the Action Teams and with children participating in the interventions. Empowerment of children is evaluated during focus groups. Summaries and transcripts of meetings are coded and analysed to enrich children's findings. Ethics and dissemination The Medical Ethics Committee of the VU Medical Center approved the study protocol (2016.366). Trial registration number TC=6604.