Abstract Background The importance and pathophysiology of transmural healing in patients with Crohn’s disease [CD] remains to be verified. We aimed to examine the association between serum concentrations of biologics and transmural remission evaluated via magnetic resonance enterography [MRE]. Methods We enrolled patients with CD who received maintenance biologics 1 year after induction and prospectively followed up for at least 1 year after baseline laboratory, endoscopic and MRE examination. We evaluated the relationship between baseline factors including the presence of transmural remission and patient prognosis, as well as between serum concentrations and transmural remission. Results We included 134 patients, of whom 65, 31, 27 and 11 received infliximab, adalimumab, ustekinumab and vedolizumab, respectively. Those who achieved transmural remission showed a lower risk of hospitalization and surgery than those who did not achieve remission [p < 0.01]. Adjusted hazard ratios of transmural remission for predicting hospitalization and surgery were 0.11 and 0.02, respectively, which were lower than those of clinical remission, biochemical remission and endoscopic remission. Regarding serum concentrations, the median concentration was higher in patients with transmural remission than in patients with transmural activity for all agents [p < 0.01 for infliximab, p = 0.04 for adalimumab, p < 0.01 for ustekinumab, p = 0.08 for vedolizumab]. Conclusions Transmural remission was the best predictor for prognosis in CD patients who received maintenance biologic therapy. High drug concentration levels were associated with transmural remission confirmed via MRE.