Abstract Introduction Recurrent Clostridium difficile infection (CDI) is common and often difficult to manage. Faecal microbiota transplant (FMT) is an effective therapeutic tool in these cases, although its applicability and effectiveness in Spain is currently unknown. Aim To analyse the technical aspects, safety and effectiveness of the first consolidated FMT programme in Spain. Methods Retrospective descriptive study of all patients with recurrent CDI treated with FMT performed by colonoscopy in a tertiary centre after the implementation of a multidisciplinary protocol between March 2015 and September 2016. Results A total of 13 FMT were performed in 12 patients (11/12; 91.7% women) with a median age of 84.6 years (range: 38.2–98.2). Recurrence of CDI was the indication for FMT in all cases. Patients had suffered a median of 3 previous episodes of CDI (range: 2–6) and all had failed treatment with fidaxomicin. All procedures were performed by colonoscopy. Effectiveness with one session of FMT was 91.7% (11/12; 95% CI: 64.6–98.5%). In the non-responder patient, a second FMT was performed 17 days after the first procedure, with disappearance of symptoms. No side effects related to the endoscopic procedure or the FMT were recorded after a median follow-up of 6.5 months (range: 1–16 months). Two patients died during follow-up due to causes unrelated to FMT. Conclusion FMT by colonoscopy is an effective and safe therapeutic alternative in recurrent CDI. It is a simple procedure that should be implemented in more centres in Spain.