The negative role of malnutrition in patients with Crohn’s disease is known; however, many coexisting disease-related factors could cause misinterpretation of the real culprit. This study aimed to describe the role of malnutrition using a novel methodology, entropy balancing. This was a retrospective analysis of consecutive patients undergoing elective major surgery for Crohn’s disease, preoperatively screened following the European Society for Clinical Nutrition guidelines. Two-step entropy balancing was applied to the group of malnourished patients to obtain an equal cohort having a null or low risk of malnutrition. The first reweighting homogenised the cohorts for non-modifiable confounding factors. The second reweighting matched the two groups for modifiable nutritional factors, assuming successful treatment of malnutrition. The entropy balancing was evaluated using the d-value. Postoperative results are reported as mean difference or OR, with a 95 % CI. Of the 183 patients, 69 (37·7 %) were at moderate/high risk for malnutrition. The malnourished patients had lower BMI (d = 1·000), Hb (d = 0·715), serum albumin (d = 0·981), a higher lymphocyte count (d = 0·124), Charlson Comorbidity Index (d = 0·257), American Society of Anaesthesiologists (d = 0·327) and Harvey-Bradshaw scores (d = 0·696). Protective loop ileostomy was more frequently performed (d = 0·648) in the malnourished group. After the first reweighting, malnourished patients experienced a prolonged length of stay (mean difference = 1·9; 0·11, 3·71, days), higher overall complication rate (OR 4·42; 1·39, 13·97) and higher comprehensive complication index score (mean difference = 8·9; 2·2 15·7). After the second reweighting, the postoperative course of the two groups was comparable. Entropy balancing showed the independent role of preoperative malnutrition and the possible advantages obtainable from a pre-habilitation programme in Crohn’s disease patients awaiting surgery.