BACKGROUND: Coronavirus disease 2019 (COVID-19) is often accompanied by gastrointestinal symptoms, which is related to gut microbiota dysbiosis (GMD). Whether washed microbiota transplantation (WMT) is effective in COVID-19 patients suspected with GMD by restoring gut microbiota is unknown. This study is designed to explore the efficacy and safety of WMT in COVID-19 patients suspected with GMD.METHODS: COVID-19 patients suspected with GMD will be randomly divided to receive routine treatment (group A) or receive routine treatment and WMT (group B). The frequency of WMT will be once a day for three consecutive days. Nucleic acid test, imaging examination, and tests related to organ functions, homeostasis, inflammatory response, intestinal barrier function and immunity will be performed at admission, 1, and 2 weeks after treatment and on the day of discharge. The clinical efficacy and safety of WMT in COVD-19 suspected with GMD and the effects of WMT on the organ function, homeostasis, inflammatory response, intestinal barrier function and immunity of the patients will be evaluated. The primary outcome will be the clinical efficacy, as reflected by the SARS-Cov-2 infection status, gastrointestinal symptoms and the recovery of the disease. The secondary outcomes will be the effects of WMT on the organ function, homeostasis, inflammatory response, intestinal barrier function and immunity of the patients, as well as occurrence of adverse events during WMT.DISCUSSION: In the proposed protocol, WMT is expected to be efficacious and safe for the treatment of COVID-19 patients suspected with GMD, and the therapeutic effect is expected to be associated with the improvement of intestinal barrier function, inflammatory response and immunity. Findings from this study may open up a new way for the prevention and treatment of COVID-19 suspected with GMD.TRIAL REGISTRATION: Chinese Clinical Trial Registry – URL: http://www.chictr.org.cn/index.aspx. Registration number: ChiCTR2000032737. Registered 9 May 2020.