Background Crohn’s disease (CD) is a progressive, destructive, and disabling disorder. Our study aimed to assess changes over time in the Lémann index (LI) and the Inflammatory Bowel Disease Disability Index (IBD-DI) in a cohort of CD patients. Methods This was a single-center prospective cohort study of 130 consecutive CD patients with a follow-up of at least 4 years. The LI 1 and the IBD-DI 1 questionnaires were assessed in 2016 and again between September 2020 and October 2021 (LI 2 and IBD-DI 2). Results Of the 130 patients with assessment of both LI 1 and IBD-DI 1, 61 had calculation of the LI 2 and 98 patients answered the IBD-DI 2 questionnaire, with a median time between the 2 evaluations of 4.2 years. The LI increased for 16 (26%), decreased for 26 (43%), and remained unchanged for 19 (31%) patients. The median LI did not change over time (9.6 vs 9.3; P = .14). Clinical disease activity was significantly associated with bowel damage progression. A high initial LI (>7.9) was not associated with CD progression (surgery, drug dose escalation, or change of biologic). The IBD-DI decreased for 59 (60.2%), increased for 37 (37.8%), and remained unchanged for 2 (2%) patients. The median IBD-DI decreased significantly over time (23.2 vs 21.4; P = .006). There was no correlation between the 2 indexes. Conclusions This is the first prospective cohort study assessing changes over time in both the LI and the IBD-DI in CD patients. After 4 years, the LI appeared to be stable and the IBD-DI decreased, with no correlation between the 2 indexes.