ObjectiveThe purpose of this study was to investigate the impact of obesity on disease activity and disease outcome in patients with inflammatory bowel disease.Patients and methodsThe impact of obesity on inflammatory bowel disease disease activity and outcome was retrospectively assessed in 3075 patients enrolled in the prospective nation‐wide Swiss inflammatory bowel disease cohort between July 2006 and September 2018. Baseline characteristics, disease activity and disease course in 325 obese inflammatory bowel disease patients (body mass index ≥30 kg/m2) were compared to 1725 normal weight inflammatory bowel disease individuals (body mass index 18.5‐24.9).ResultsAmong 3075 patients in the prospective Swiss inflammatory bowel disease cohort, 325 patients (10.6%) were obese, namely, 194 Crohn’s disease patients, 131 ulcerative colitis, and inflammatory bowel disease‐unclassified patients. Disease activity scores were elevated in obese Crohn’s disease (Crohn’s Disease Activity Index 33 vs 20, p = 0.001), but not ulcerative colitis patients. Obese Crohn’s disease, but not ulcerative colitis patients were less likely to be in remission based on a Crohn’s Disease Activity Index less than 100 and a calprotectin less than 100 ug/g. In a multivariate regression model, obesity was negatively associated with disease remission in Crohn’s disease (odds ratio 0.610, 95% confidence interval 0.402–0.926, p = 0.020), but not ulcerative colitis. Increased soft stool frequency was observed in both obese Crohn’s disease and ulcerative colitis patients. Adjusted Cox regression models revealed increased risk of complicated disease course in obese Crohn’s disease patients (hazard ratio 1.197, 95% confidence interval 1.046–1.370, p = 0.009). No association between obesity and disease progression, index treatment failure was seen neither in Crohn’s disease nor ulcerative colitis.ConclusionObesity is associated with decreased rates of disease remission and increased risk of complicated disease course in Crohn’s disease over a six‐year follow‐up period. No effects were seen on disease progression and index treatment failure neither in Crohn’s disease nor ulcerative colitis.