Background: The outcomes of bariatric surgery (BS) in patients with chronic inflammatory bowel disease (IBD) remain rarely described. We aimed to evaluate the 90-day morbidity and mortality rates, and the risk of IBD complications 2 years after BS. Method: Patients from the French Programme de Médicalisation des Systèmes d’Information (PMSI) database who underwent a primary BS between 2016 and 2018 were included. We identified patients with a previous diagnosis of IBD. Postoperative 90-day (POD90) morbidity and mortality rates were compared between the two groups. The evolution of IBD was followed 2 years after BS. Results: Between 2016 and 2018, 138 980 patients underwent primary BS, including 587 patients with IBD: 326 (55.5 per cent) with Crohn’s disease (CD) and 261 (44.5 per cent) with ulcerative colitis (UC). The preferred surgical technique was sleeve gastrectomy, especially in the IBD group (81.1 per cent), followed by gastric bypass (14.6 per cent). Patients with IBD had more comorbidities (Charlson Comorbidity Index of 1 or more, hypertension, and diabetes; P < 0.001) than those without IBD. The POD90 mortality rate did not differ between the two groups (0.049 per cent in the IBD group versus 0 per cent in the non-IBD group), but more unscheduled rehospitalizations at POD90 were observed in patients with IBD (6.0 per cent versus 3.7 per cent; P = 0.004). Two years after BS, 86 patients (14.6 per cent) in the IBD group had at least one unplanned readmission for the management of their IBD; 15 patients stayed for 3 or more days. After multivariable analysis, patients with CD had an independent elevated risk of IBD-related unplanned readmissions 2 years after BS versus UC (adjusted odds ratio 1.90, 95 per cent c.i. 1.22 to 2.97; P = 0.005). Conclusion: In a highly selected cohort of patients with well-controlled IBD, BS did not result in added mortality or morbidity. A point of vigilance must be underlined regarding BS in patients with CD.