In children with mild-to-moderate Crohn’s disease, exclusive enteral nutrition (EEN) is recommended but challenging to implement. In a 12-week prospective randomized controlled trial, 78 children with Crohn’s disease were assigned to either receive the Crohn’s disease exclusion diet (CDED) plus 50% of calories from formula for 6 weeks followed by CDED plus 25% partial enteral nutrition (PEN) for a further 6 weeks, or to receive EEN for 6 weeks and then a free diet plus PEN for a further 6 weeks. The combination of CDED plus PEN was found to be better tolerated than EEN. Although both diets were found to induce corticosteroid-free remission by week 6, the combination of CDED plus PEN led to sustained remission in significantly (P = 0.01) more patients than EEN at week 12. The CDED plus PEN combination also led to changes in the faecal microbiome that were associated with remission, further supporting this approach in children with Crohn’s disease.