Faecal microbiota transplantation (FMT) has evolved from a marginal concept to a prevalent therapeutic intervention, particularly for individuals with recurrent Clostridioides difficile infection (CDI). FMT addresses the root cause of dysbiosis, a critical aspect of CDI pathogenesis, by re-establishing a healthy intestinal microbiota via the transplantation of donor stool. The objective of this mini review is to provide an overview of the history of faecal microbiota transplantation (FMT), encompassing its clinical validation, regulatory progression, evolving safety profile, and emerging position in next-generation microbial therapies. A comprehensive literature review was conducted using databases such as PubMed, Scopus, and Web of Science to identify peer-reviewed studies, clinical trials, and regulatory documents on faecal microbiota transplantation (FMT). Selection focused on sources addressing clinical efficacy, safety, regulatory status, and emerging microbial therapies for recurrent Clostridioides difficile infection. Faecal microbiota transplantation (FMT) has a cure rate over 90% in certain studies, and can be administered by several methods. The FDA has granted conditional regulatory approval within its enforcement discretion. Although FMT shows high success rates, there are increasing concerns about the risk of transmitting harmful bacteria—such as STEC and EPEC—and the uncertain long-term effects these microbes may have on the recipient’s gut health and immune system. Researchers are currently concentrating on standardized microbial consortia that may more precisely and securely reproduce the advantages of faecal microbiota transplantation (FMT). FMT represents a significant shift in the treatment of CDI and has paved the way for microbiome-based medicine. Long-term safety surveillance, explicit protocols, and the development of precisely specified microbial therapies will be crucial for future success.