Introduction Involving patients in decision making is a legal requirement in many countries, associated with better rehabilitation outcomes, but not easily accomplished during initial inpatient rehabilitation after severe trauma. Providing medical treatment according to the principles of shared decision making is challenging as a point in case for persons with spinal cord injury (SCI). Objectives The aim of this study was to retrospectively explore the patients’ views on their participation in decision making during their first inpatient rehabilitation after onset of SCI, in order to optimize treatment concepts. Methods A total of 22 participants with SCI were interviewed in‐depth using a semi‐structured interview scheme between 6 months and 35 years post‐onset. Interviews were transcribed verbatim and analysed with the Mayring method for qualitative content analysis. Results Participants experienced a substantially reduced ability to participate in decision making during the early phase after SCI. They perceived physical, psychological and environmental factors to have impacted upon this ability. Patients mentioned regaining their ability to make decisions was an important goal during their first rehabilitation. Receiving adequate information in an understandable and personalized way was a prerequisite to achieve this goal. Other important factors included medical and psychological condition, personal engagement, time and dialogue with peers. Conclusion During the initial rehabilitation of patients with SCI, professionals need to deal with the discrepancy between the obligation to respect a patient's autonomy and their diminished ability for decision making.