Background Today, the increasing demand for complementary medicine encourages health care providers to adapt and create integrative medicine departments or services within clinics. However, because of their differing philosophies, historical development, and settings, merging the partners (conventional and complementary medicine) is often difficult. It is necessary to understand the similarities and differences in both cultures to support a successful and sustainable integration. The aim of this project was to develop a theoretical model and practical steps that are based on theories from mergers in business to facilitate the implementation of an integrative medicine department. Methods Based on a literature search and expert discussions, the cultures were described and model domains were developed. These were applied to two case studies to develop the final model. Furthermore, a checklist with practical steps was devised. Results Conventional medicine and complementary medicine have developed different corporate cultures. The final model, which should help to foster integration by bridging between these cultures, is based on four overall aspects: culture, strategy, organizational tools and outcomes. Each culture is represented by three dimensions in the model: corporate philosophy (core and identity of the medicine and the clinic), patient (all characteristics of the professional team’s contact with the patient), and professional team (the characteristics of the interactions within the professional team). Conclusion Overall, corporate culture differs between conventional and complementary medicine; when planning the implementation of an integrative medicine department, the developed model and the checklist can support better integration.