Purpose End-ileostomy after two-staged ileocolic resection is frequently performed in Crohn’s disease patients at high risk for postoperative complications. However, there is paucity on data regarding the morbidity after the stoma reversal. Methods One hundred thirty patients undergoing closure of end-ileostomy between 1994 and 2016 were included. Data collection was retrospective in 11 first, and it was prospective in 119 last patients. Anastomotic complications were defined as anastomotic leak, perianastomotic abscess, and perianastomotic peritonitis. Results The median interval between ileostomy construction and reversal was 4.0 months. Ninety-seven of 121 patients with available data (80%) gained weight between both surgeries. Hemoglobin level increased between surgeries in 107 patients (85%). Fifteen patients (11.5%) received parenteral fluid substitution or parenteral nutrition between both surgeries. There were 37 hospital readmissions during the time between stoma construction and reversal (29%). After ileostomy reversal, 14 patients developed anastomotic complications (11%). By multivariate regression analysis, preoperative steroid intake (hazard ratio 4.5, 95% CI: 1.11–18.0, p  = 0.035) and hospital readmission for infectious complications (HR 4.5, 95% CI: 1.11–18.0, p = 0.035) were statistically significantly associated with an increased risk to develop postoperative anastomotic complications. There were no postoperative deaths. Conclusion Closure of end-ileostomy could be complicated by some serious morbidity. These risks should be taken into consideration weighing carefully between the one- and two-stage ileocolic resection in Crohn’s disease patients.