Little data are available regarding the effectiveness and associated microbiome changes of faecal microbiota transplantation (FMT) for Clostridium difficile infection (CDI) in children, especially in those with inflammatory bowel disease (IBD) with presumed underlying dysbiosis.

To investigate C. difficile eradication and microbiome changes with FMT in children with and without IBD.

Children with a history of recurrent CDI (≥3 recurrences) underwent FMT via colonoscopy. Stool samples were collected pre‐FMT and post‐FMT at 2–10 weeks, 10–20 weeks and 6 months. The v4 hypervariable region of the 16S rRNA gene was sequenced. C. difficile toxin B gene polymerase chain reaction was performed.

Eight children underwent FMT for CDI; five had IBD. All had resolution of CDI symptoms. All tested had eradication of C. difficile at 10–20 weeks and 6 months post‐FMT. Pre‐FMT patient samples had significantly decreased bacterial richness compared with donors (P = 0.01), in those with IBD (P = 0.02) and without IBD (P = 0.01). Post‐FMT, bacterial diversity in patients increased. Six months post‐FMT, there was no significant difference between bacterial diversity of donors and patients without IBD; however, bacterial diversity in those with IBD returned to pre‐FMT baseline. Microbiome composition at 6 months in IBD‐negative patients more closely approximated donor composition compared to IBD‐positive patients.

FMT gives sustained C. difficile eradication in children with and without IBD. FMT‐restored diversity is sustained in children without IBD. In those with IBD, bacterial diversity returns to pre‐FMT baseline by 6 months, suggesting IBD host‐related mechanisms modify faecal microbiome diversity.