Patients with inflammatory bowel disease (IBD) are at increased risk of developing Clostridium difficile infection (CDI). Fecal microbiota transplantation (FMT) is an effective therapy with a high success rate in preventing recurrent CDI. However, patients with IBD have decreased response to FMT for recurrent CDI, with several reports also suggesting potential IBD flare post-FMT. We present a case of mild ileocolonic Crohn's disease in a patient treated with FMT for recurrent CDI who subsequently developed severe steroid-refractory flare requiring surgical intervention 1 week post-FMT. Greater understanding of risk factors associated with post-FMT IBD flare is indicated.