Objectives: The global scientific community is struggling to understand the features of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and its related disease (coronavirus disease-2019, COVID-19). Even if the main symptoms of COVID-19 are respiratory, gastrointestinal manifestations have been described too. The disease shows a highly variable clinical course, from asymptomatic cases to lethal ones. Scientists are questioning the reasons that may explain these different disease courses. It is reasonable to speculate that the intestinal and pulmonary microbiota, and their mutual interaction in the “gut-lung axis”, might influence the severity of COVID-19. In this context, the modification of the microbiota through fecal microbiota transplantation (FMT) might constitute a rescue therapy. Unfortunately, no randomized clinical trial has been conducted to prove the efficacy of FMT in COVID-19 patients and its role is only potential; to date, FMT is only recommended for recurrent infections of Clostridium difficile. Since the risk of transmission of SARS-CoV-2 with cells, tissues, and organs has not been demonstrated but cannot be excluded, many authorities have proposed stricter screening measures for donors. FMT is a potential means of SARS-CoV-2 transmission and the spread of the virus is creating concern among FMT experts worldwide. This review explores the “two sides of a coin”, analyzing both the potential applications of FMT during COVID-19, also by revising the role of the microbiota during the infection and by discussing the limitations to FMT that have emerged during the pandemic and the proposal of the scientific community to overcome them.