Background The development of professionalism is one of the fundamental goals of educational systems, especially in medical sciences. Medical students, in addition to acquiring clinical knowledge and skills, should somehow benefit from moral values and professionalism in order to practice in a professional manner. The development of professional ethics is heavily influenced by the hidden curriculum affected by changes in the educational system. The health reform plan is launched in Iran in recent years. Objectives The current study aimed at qualitatively explaining the effects of changes to the educational system on the development of the professionalism in medical residents. Methods The current qualitative study was performed by the content analysis method. A total of 26 interviews were conducted with 12 prominent professors of medical education, 13 third-year internal medicine residents, as well as a focus group including 10 residents. The purposive sampling method with maximum diversity was used in the current study and continued until data saturation. Data were analyzed using the content analysis method. The Lincoln and Guba criteria were used to increase the credibility of the findings. Results The most important finding of the current study was the challenge of developing professionalism due to environmental changes. The main theme included the challenges of professionalism development in the existing educational system, changes related to the sociocultural environment of the community, changes related to health reform plan, and the shift from training to health services and promtion of faculty member. Conclusions Changes and interventions in the health care services sector, such as the health reform plan, greatly affect the development of professionalism in medical residents. The plans that affect the health system, a special attention should be paid to the education section and the educational documents should be prepared initially and implemented simultaneously.