Introduction and objective: The announcement of a world pandemic of COVID-19 has placed the modern healthcare systems in a new, unprecedented situation, unencountered in the past century. Rapid introduction of guidelines and standards regarding reorganization of healthcare systems was required. A massive occurrence of infections with respiratory failure resulted in overcrowding of infectious disease wards and the necessity to open new temporary infectious disease wards and field hospitals worldwide, in places that were often not prepared for this type of medical activity. The development of diagrams of conduct in accordance with business procedures (BPMN2.0) with a clear definition of the scope of responsibility seems in such situations a guarantee of maintaining an optimal level of safety for all participants of the diagnostic and therapeutic process. The aim of the study: to develop the Emergency Department and the COVID-19 Unit functioning model in accordance with the BPMN2.0 business process protocol and its verification based on the system and structure functioning at the University Clinical Hospital No1 in Lodz. Results: The authors created a standard notation protocol for the process of dealing with a patient in the Emergency Department/ Admission Room and the COVID-19 Unit, and then verified the model based on their own experience, gathered during the creation and running of a temporary COVID-19 Unit with an Isolation Area. Conclusions: The development of treatment algorithms in the field of medicine in accordance with business procedures based on the BPNM2.0 protocol is the basis for the smooth operation of medical personnel with the determination of the scope of duties and responsibilities. The use of standardized procedures for working with a suspected or confirmed patient with SARS-CoV-2 infection in the area of ED and COVID-19 Unit when crossing individual risk zones of SARS-CoV-2 infection allows for maintaining appropriate epidemiological standards.