Although useful in preventing recurrent Clostridium difficile infection (RCDI), whether the clinical effectiveness of faecal microbiota transplantation (FMT) is altered by delivery route was previously unknown. In a multicentre, randomized controlled trial, 116 adults with RCDI randomly received FMT by either oral capsule or colonoscopy. After 12 weeks, 92.6% of patients in both groups achieved prevention of RCDI after a single treatment. Minor adverse events were less frequent in the capsule group (5.4%) than the colonoscopy group (12.5%), and a greater proportion of participants in the capsule group rated the procedure as “not at all unpleasant”. These findings demonstrate that FMT via oral capsules is effective for treating RCDI and is not inferior to delivery by colonoscopy.