Background: The prevalence of mental health problems in childhood and adolescence has increased significantly, not least due to the COVID-19 pandemic in Germany and other countries worldwide. Although holistic school interventions to promote mental health and prevent mental health problems are considered promising, there is currently uncertainty about their effectiveness due to evaluation studies with heterogeneous methodological quality. This paper presents the study protocol for the evaluation of the primary school module of MindMatters. Methods: As part of a universal mental health intervention, the MindMatters primary school module ‘Learning Together with Emotions’ aims to promote social-emotional learning (SEL) in the classroom across five skill areas. In addition to classroom activities, the intervention includes a school development module to help primary schools create structures and processes to maintain and promote mental health. To evaluate the effectiveness of the intervention, a two-arm cluster-randomised controlled trial will be conducted, including schools implementing MindMatters over a 12-month period and a control group with no access to the intervention. Data will be collected before and 18 months after initiation of the intervention. Controlled for baseline conditions, multilevel regression analysis will be used to examine primary intervention outcomes at the pupil level (i.e. reductions in mental and behavioural problems). Further mediation and moderation analyses will examine whether proximal outcomes predict changes in mental health outcomes and whether school-level factors influence the effectiveness of the intervention. Discussion: This study will contribute to strengthen the evidence base for holistic school (mental) health promotion interventions using a study design with high internal validity. Based on an intervention model, the results will not only provide insights into the relationship between proximal and distal outcomes, but will also allow conclusions to be drawn about how the implementation of the intervention affects its effectiveness. Finally, the findings also address the question of whether improved mental health has a positive effect on primary school pupils’ academic performance. Trial registration: German Clinical Trials Register DRKS00023762. Registered on 5 January 2021.