Summary Background and Aims Magnetic resonance enterography (MRE) depicts transmural changes in response to biological treatment for Crohn's disease (CD); however, the long‐term prognostic significance of these findings is unknown. The primary objective of this study was to identify findings on MRE 46 weeks after initiating biological treatment that predict adverse long‐term outcomes. Methods Patients with CD underwent MRE 46 weeks after initiating biological treatment and were prospectively followed for 2 years. A logistic regression analysis was performed to assess the prognostic value of different radiologic findings for various predefined adverse outcomes. Results Of the 89 patients included, 46 (51.7%) had ≥1 adverse outcome during follow‐up: 40 (44.9%) had clinical recurrence; 18 (20.2%) required surgery, 8 (9%) endoscopic balloon dilation, 12 (13.5%) hospitalization and 7 (7.8%) required corticosteroids. In the multivariate analysis, persistence of severe lesions (MaRIA ≥11) in any intestinal segment was associated with an increased risk of surgery [OR 11.6 (1.5–92.4)], of surgery and/or endoscopic balloon dilation [OR 6.3 (1.3–30.2)], and of clinical relapse [OR 4.6 (1.6–13.9)]. Penetrating lesions were associated with surgery [OR 3.4 (1.2–9.9)]. Creeping fat with hospitalization [OR 5.1 (1.1–25.0)] and corticosteroids requirement [OR 16.0 (1.2–210.0)]. The presence of complications (stricturing and/or penetrating lesions) was associated with having ≥1 adverse outcome [OR 3.35 (1.3–8.5)]. Conclusion MRE findings at week‐46 after initiating biological therapy can predict long‐term adverse outcomes in CD. Therapeutic intervention may be required in patients with persistence of severe inflammatory lesions, CD‐associated complications, or creeping fat.