Anastomotic leakage (AL) after colorectal resections is a serious complication in abdominal surgery. Especially in patients with Crohn’s disease (CD), devastating courses are observed. Various risk factors for the failure of anastomotic healing have been identified; however, whether CD itself is independently associated with anastomotic complications still remains to be validated. A retrospective analysis of a single-institution inflammatory bowel disease (IBD) database was conducted. Only patients with elective surgery and ileocolic anastomoses were included. Patients with emergency surgery, more than one anastomosis, or protective ileostomies were excluded. For the investigation of the effect of CD on AL 141, patients with CD-type L1, B1–3 were compared to 141 patients with ileocolic anastomoses for other indications. Univariate statistics and multivariate analysis with logistic regression and backward stepwise elimination were performed. CD patients had a non-significant higher percentage of AL compared to non-IBD patients (12% vs. 5%, p = 0.053); although, the two samples differed in terms of age, body mass index (BMI), Charlson comorbidity index (CCI), and other clinical variables. However, Akaike information criterion (AIC)-based stepwise logistic regression identified CD as a factor for impaired anastomotic healing (final model: p = 0.027, OR: 17.043, CI: 1.703–257.992). Additionally, a CCI ≥ 2 (p = 0.010) and abscesses (p = 0.038) increased the disease risk. The alternative point estimate for CD as a risk factor for AL based on propensity score weighting also resulted in an increased risk, albeit lower (p = 0.005, OR 7.36, CI 1.82–29.71). CD might bear a disease-specific risk for the impaired healing of ileocolic anastomoses. CD patients are prone to postoperative complications, even in absence of other risk factors, and might benefit from treatment in dedicated centers.