Purpose To gain insight into factors enhancing or obstructing implementation in various school-settings, which is vital for widespread dissemination and sustainable integration of school-based health-promoting interventions. Design/methodology/approach A mixed methods multisite comparative case study to investigate (factors influencing) the implementation of health-promoting activities in twelve Dutch primary schools. Data were collected during three school years (2019–2022) through observations, questionnaires and interviews. Findings The project resulted in the implementation of small, incidental activities. Important reasons for the limited implementation were lack of commitment and bottom-up involvement. School directors and teachers were not involved early on in the project, which limited project support and commitment. On school level, directors largely carried project responsibility themselves, hindering project sustainability and integration. Coronavirus disease 2019 (COVID-19) made that schools had difficulties forming long-term visions and plans. Other observed barriers included limited perceived necessity to change, high workload and high staff turnover. Important facilitators were the presence of a process coordinator and sharing experiences from other schools. Originality/value This research provided valuable insights into (factors influencing) the implementation of health-promoting initiatives in diverse, real-world school contexts. More extensive support is needed to create commitment, bottom-up involvement and a project vision. Furthermore, empowering in-school champions and/or school-wide project groups is desirable to decrease schools' dependence on long-term external support. The findings can be used by various stakeholders throughout development, adoption and implementation and can facilitate widespread dissemination and sustainable integration of school-based health-promoting interventions.