Severe cases infected with the coronavirus disease 2019 (COVID-19), named by the World Health Organization (WHO) on Feb. 11, 2020, tend to present a hypercatabolic state because of severe systemic consumption, and are susceptible to stress ulcers and even life-threatening gastrointestinal bleeding. Endoscopic diagnosis and treatment constitute an irreplaceable part in the handling of severe COVID-19 cases. Endoscopes, as reusable precision instruments with complicated structures, require more techniques than other medical devices in cleaning, disinfection, sterilization, and other reprocessing procedures. From 2016 to 2019, health care-acquired infection caused by improper endoscope reprocessing has always been among the top 5 on the list of top 10 health technology hazards issued by the Emergency Care Research Institute. Considering the highly infective nature of COVID-19 and the potential aerosol contamination therefrom, it is of pivotal significance to ensure that endoscopes are strictly reprocessed between uses. In accordance with the national standard “Regulation for Cleaning and Disinfection Technique of Flexible Endoscope (WS507-2016),” we improved the workflow of endoscope reprocessing including the selection of chemicals in an effort to ensure quality control throughout the clinical management towards COVID-19 patients. Based on the experience we attained from the 12 severe COVID-19 cases in our hospital who underwent endoscopy 23 times in total, the article provides an improved version of endoscopic reprocessing guidelines for bedside endoscopic diagnosis and treatment on COVID-19 patients for reference.