Given today’s high prevalence of common mental disorders and related sick leave among teachers, an urgent need exists for a more systematic approach to the management of social and organizational risk factors within schools. In 2015, we launched the first Swedish occupational health guideline to support a structured prevention of these risks at the workplace. The existence of guidelines does however not guarantee their usage, as studies show that guidelines are often underused. Knowledge is therefore needed on effective implementation strategies that can facilitate the translation of guidelines into practice. The primary aim of the randomized waiting list-controlled trial described in this study protocol is to compare the effectiveness of a multifaceted implementation strategy versus a single implementation strategy for implementing the Guideline for the prevention of mental ill-health at the workplace within schools. The effectiveness will be compared regarding the extent to which the recommendations are implemented (implementation effectiveness) and with regard to social and organisational risk factors for mental ill-health, absenteeism and presenteeism (intervention effectiveness).