Background: The emergency department is the first and foremost part of the hospital, which is responsible for accepting and categorizing patients quickly in various crises. In the covid-19 pandemic, designing appropriate procedures and facilities for triage, diagnosis and isolation of suspected and confirmed cases was a high priority for hospital emergencies. Methods: In a retrospective cross-sectional study from March 2019 to the beginning of April 2022, patients' clinical symptoms were evaluated and analyzed during the protocols issued by the Ministry of Health in Iran. Results: Since the beginning of the pandemic and following the changes in the conditions and new national and international shreds of evidence, Iran's Ministry of Health has issued more than 11 guidelines in different areas of education, health and treatment. This paper analyzes the course of changes in these guidelines and the management of specific populations during the pandemic. Conclusion: Risk stratification in patients based on underlying diseases, current clinical status, and availability of hospital resources is one of the most important measures of health systems. Paying attention to biological points in different wards and patient management from triage to appropriate diagnosis and treatment, Prioritizing and allocating resources, proper use of personal protective equipment in medical staff, were important.