BackgroundAccreditation is a prerequisite for scientific management of the health system, owing to its numerous benefits on health centres’ performance. The current study examined Iran’s primary healthcare accreditation program to ascertain the challenges to its successful implementation.MethodsThis qualitative study examined the perspectives of 32 managers and staff members in the pilot accreditation program (from the Ministry of Health and Medical Education, Semnan University of Medical Sciences, and Aradan District Health Network). Three in-depth group interviews were conducted using a semi-structured questionnaire, and the data obtained were assessed using thematic analysis. As a result of this investigation identified six themes, 29 sub-themes, and 218 codes as challenges to the successful accreditation of primary health care in Iran.ResultsSix main themes, including “organisational culture”, “motivational mechanisms”, “staff workload”, “training system”, “information systems”, and “macro-executive infrastructure”, were identified as the main domain of challenges, with seven, five, two, four, three, and eight sub-themes respectively.ConclusionAccreditation of PHC in Iran faces significant challenges and obstacles that, if ignored, can jeopardise the program’s success and effectiveness. By identifying challenges and obstacles and making practical suggestions for overcoming them, the findings of this study can aid in the program’s successful implementation and achievement of desired outcomes.