For implementation of patient-centered treatment in interprofessional health care units, such as rehabilitation teams, external participation (interaction between patient and health care professionals) and internal participation (communication, coordination and cooperation in the interprofessional team) need to be considered. The aim of this study is to identify the preferences of patients and health care professionals concerning internal and external participation in rehabilitation clinics, in order to develop an interprofessional shared decision-making (SDM) training program for health care professionals to enhance both types of participation. Therefore, a cross-sectional mixed-methods study was implemented in four rehabilitation clinics. The study consists of two parts: focus groups with patients and a survey of experts (senior health care professionals from medicine, psychotherapy, physical therapy and nursing). More time, more respect from the health care professionals and the desire for more participation in decision-making processes were mentioned most frequently by patients (n = 36) in the focus groups. The health care professionals (n = 32) saw most deficits in internal participation, e. g. management of feedback, talking with difficult team members and moderate conflict discussion. The results of both assessments have been used to develop an interprofessional SDM training program for implementing internal and external participation in interprofessional teams in medical rehabilitation.