Clinical decision support systems (CDSSs) are increasingly being introduced into various domains of health care. Little is known so far about the impact of such systems on the health care professional-patient relationship, and there is a lack of agreement about whether and how patients should be informed about the use of CDSSs. This study aims to explore, in an empirically informed manner, the potential implications for the health care professional-patient relationship and to underline the importance of this relationship when using CDSSs for both patients and future professionals. Using a methodological triangulation, 15 medical students and 12 trainee nurses were interviewed in semistructured interviews and 18 patients were involved in focus groups between April 2021 and April 2022. All participants came from Germany. Three examples of CDSSs covering different areas of health care (ie, surgery, nephrology, and intensive home care) were used as stimuli in the study to identify similarities and differences regarding the use of CDSSs in different fields of application. The interview and focus group transcripts were analyzed using a structured qualitative content analysis. From the interviews and focus groups analyzed, three topics were identified that interdependently address the interactions between patients and health care professionals: (1) CDSSs and their impact on the roles of and requirements for health care professionals, (2) CDSSs and their impact on the relationship between health care professionals and patients (including communication requirements for shared decision-making), and (3) stakeholders' expectations for patient education and information about CDSSs and their use. The results indicate that using CDSSs could restructure established power and decision-making relationships between (future) health care professionals and patients. In addition, respondents expected that the use of CDSSs would involve more communication, so they anticipated an increased time commitment. The results shed new light on the existing discourse by demonstrating that the anticipated impact of CDSSs on the health care professional-patient relationship appears to stem less from the function of a CDSS and more from its integration in the relationship. Therefore, the anticipated effects on the relationship between health care professionals and patients could be specifically addressed in patient information about the use of CDSSs.