Introduction: This study aimed to explore the challenges of professional identity formation at clinical education environments from the faculty members’ viewpoints. Methods: This is a qualitative study. The population consisted of clinical faculty members of Tehran University of Medical Sciences. In this study, 39 faculty members participated in an in-depth semi-structured interview. To analyze the data, conventional content analysis approach was used. Open coding was extracted from the participants’ statements that represented their experiences. Then, based on their similarities, the codes were classified. Subcategories were emerged and after arranging, they were classified into categories based on their relationships. Results: Instability of professional commitment, patientcenteredness as the missing loop care and treatment, and inappropriate conductive context were explored as the challenges of professional identity in clinical educational environment. Conclusion: According to the results of the study, the formation of professional identity among the providers is not an easy task because many factors affect the formation of professional identity. Therefore, a comprehensive shift towards forming the professional identity at individual and organizational level should be planned.