Purpose The global prevalence of inflammatory bowel disease (IBD) has steadily risen over the past few decades. Bariatric surgery stands out as an effective strategy for inducing weight loss. This study investigated the impacts of bariatric surgery on the clinical outcomes in patients with IBD. Materials and Methods Data of hospitalized patients aged ≥ 18 years with IBD were extracted from the Nationwide Inpatient Sample (NIS) 2005–2018. The patients were categorized according to whether they underwent bariatric surgery or not. Univariate and multivariable logistic regression analyses were performed to determine the associations between bariatric surgery, prolonged LOS, unfavorable discharge, hospital mortality, and morbidity. Results Data from 807,843 hospitalized patients with IBD were extracted. After exclusions and propensity-score matching, 80,545 patients were analyzed, with 16,109 undergoing bariatric surgery and 64,436 not. A total of 23% of patients had a prolonged LOS, 8% had unfavorable discharge, and the mortality rate was 1.2%. Multivariable analyses revealed that, compared to patients without bariatric surgery, patients with bariatric surgery had significantly decreased odds of prolonged LOS (adjusted odds ratio aOR, 0.89; 95% CI 0.85-0.93), unfavorable discharge (aOR, 0.83; 95% CI: 0.77-0.89), and mortality (aOR, 0.54; 95% CI: 0.44–0.67), but had increased odds of morbidity (aOR, 1.09; 95% CI 1.04–1.13). Conclusion In adults with IBD, bariatric surgery is associated with favorable outcomes concerning hospital LOS, discharge status, and mortality. However, the risk of overall morbidity is slightly increased in those who received bariatric surgery compared to those who did not. Graphical Abstract