Background Many medical students suffer from psychosocial distress and mental health problems, raising concerns about their sustainable employability and subjective wellbeing. Therefore, our faculty decided to design a wellbeing program building on the paradigm that in order to sustainably take care of others and deliver high-quality and safe patient care, (future) health professionals should take care of their own wellbeing first. The aim of our research was to design a theory-informed program on student wellbeing allowing students to acquire skills in this regard. In this paper, we describe the iterative design process and the results of our longitudinal proactive wellbeing program. Methods We conducted an educational design approach in four phases to construct the program in order to simultaneously gain new insights and develop practical solutions. We implemented the phases of educational design research over the course of two academic years. Phase 1 consisted of a review of the literature and a context and needs analysis in order to draft design principles and requirements. Phase 2 consisted of the cyclical and iterative process of design, construction and interim evaluation and adjustments of the wellbeing program (WB-program). In phase 3, evaluation and reflection, the program was implemented and evaluated. Phase 4 consisted of ongoing maturation and theoretical understanding of the program. Results With our educational design-based approach to construct a WB-program, we were able to design, construct and evaluate an evidence-informed longitudinal proactive wellbeing program for all bachelor of medicine students at our faculty. The most noteworthy result thus far is that students who are exposed to a longitudinal program with recurring attention on improving and maintaining wellbeing learn to value the importance of self-care and wellbeing and develop skills in this regard. Conclusion Taken together, our study suggests that it is possible to integrate wellbeing in a core undergraduate curriculum on a large scale. We therefore consider the results of this educational design-based development of our WB-program as a proof of concept for a longitudinal integrated program to support student wellbeing.