Pouchitis is the most common complication after restorative proctocolectomy with ileal pouch-anal anastomosis for ulcerative colitis. The authors review the role of the microbiota in both the pathogenesis of pouchitis, primarily via dysbiosis, as well as the resultant treatment strategies focused on correcting dysbiosis among patients with pouchitis. These include the role of antibiotics, probiotics, and potentially metabolomics in both treatment and risk stratification.