Faecal microbiota transplantation (FMT) has evolved from an anecdotally reported last resort for the critically ill to a well-established first-line treatment for patients with recurrent Clostridioides difficile infection (CDI), supported by grade 1a evidence. Given our improved understanding of the intestinal microbiota and how it impacts human health, FMT is now being explored for a range of emerging indications beyond CDI. In light of the rapid emergence of FMT as a novel treatment strategy in medicine, a need for international harmonisation has arisen. Addressing this need, the recently published 5th edition of the Guide to the quality and safety of tissues and cells for human application, issued by the European Directorate for the Quality of Medicines & HealthCare of the Council of Europe (EDQM), harbours complete descriptions of the collection, procurement and application of donor faeces as a substance of human origin (SoHO). The proposed revision of the Blood Tissue and Cell Regulation of the European Union (EU) incorporates stool for FMT as a SoHO. This revised regulation will provide a regulatory framework for the future development of donor-derived microbiome therapies. To implement and underpin the safety and quality requirements for FMT in this newly designed legal context, and to facilitate clinical use, collaboration and research, we established the European Academic FMT Network (EurFMT network). The European FMT Registry plays a pivotal role within this network, facilitating its clinical activities and monitoring safety. In this document, we summarise the basis for using donor faeces-derived microbiome therapies as well as the aim and main scope for the EurFMT network.