Background In the educational sector job demands have intensified, while job resources remained the same. A prolonged disbalance between demands and resources contributes to lowered vitality and heightened need for recovery, eventually resulting in burnout, sickness absence and retention problems. Until now stress management interventions in education focused mostly on strengthening the individual capacity to cope with stress, instead of altering the sources of stress at work at the organizational level. These interventions have been only partly effective in influencing burnout and well-being. Therefore, the “Bottom-up Innovation” project tests a two-phased participatory, primary preventive organizational level intervention (i.e. a participatory action approach) that targets and engages all workers in the primary process of schools. It is hypothesized that participating in the project results in increased occupational self-efficacy and organizational efficacy. The central research question: is an organization focused stress management intervention based on participatory action effective in reducing the need for recovery and enhancing vitality in school employees in comparison to business as usual? Methods/Design The study is designed as a controlled trial with mixed methods and three measurement moments: baseline (quantitative measures), six months and 18 months (quantitative and qualitative measures). At first follow-up short term effects of taking part in the needs assessment (phase 1) will be determined. At second follow-up the long term effects of taking part in the needs assessment will be determined as well as the effects of implemented tailored workplace solutions (phase 2). A process evaluation based on quantitative and qualitative data will shed light on whether, how and why the intervention (does not) work(s). Discussion “Bottom-up Innovation” is a combined effort of the educational sector, intervention providers and researchers. Results will provide insight into (1) the relation between participating in the intervention and occupational and organizational self-efficacy, (2) how an improved balance between job demands and job resources might affect need for recovery and vitality, in the short and long term, from an organizational perspective, and (3) success and fail factors for implementation of an organizational intervention.