Purpose Subtotal colectomy (STC) is performed for severe acute and refractory colitis. The diagnosis can be difficult even after the surgery when colectomy specimen has overlapping features of ulcerative colitis (UC) and Crohn’s disease (CD). The aim of this study was to evaluate the rate of postoperative diagnostic revision to CD after surgery and determine predictor factors. Methods Retrospective study of 110 patients who underwent STC (2005–2018). Results Preoperative diagnosis comprised UC = 80 (73%), CD = 11 (10%), and unclassified colitis (IBDU = 19, 17%). Initial diagnosis of IBDU and UC was modified to CD in 6 patients (6%) after STC. The final diagnosis after the follow-up of 10 ± 6 years switched from CD for 8 patients (9%). The multivariate analysis showed that patients with a colitis evolving for less than 10 years and initial diagnosis of IBDU were the two independent factors associated with an increased risk of diagnosis change to CD (p = 0.03; p = 0.016). At the end of the follow-up, 15 patients (14%) had a definitive stoma. Conclusions In patients with IBD, attention must be paid to determine the right restorative strategy to patients with an evolution of the disease less than 10 years or with IBDU who are more at risk to have a diagnosis change to CD after STC.