Autologous bone grafts for reconstruction and augmentation are routinely used for maintaining functionality and facial aesthetics. Associated complications, however, have a significant impact on patients and health care systems. This study aims to investigate the possible risk factors associated with the occurrence of complications in order to provide evidence for the outcome of autologous bone graft reconstructive procedures. Patients from 2008 to 2018 who underwent autologous (mostly mandibular) reconstruction were included in the observational study. Clinical, pathological, and therapeutic factors were examined in univariate and multivariate analysis for significance with occurring complications. A multivariate model was used to create a prognostic model predicting the occurrence of complications. Graft complications requiring revision were exhibited by 33/128 patients. Infections were most frequent, with 4/22 patients affected by multi-resistant germs. Multivariate analysis showed radiotherapy (OR = 5.714; 95% CI: 1.839–17.752; p = 0.003), obstructive pulmonary disease (OPD) (OR = 4.329; 95% CI: 1.040–18.021; p = 0.044) and length of defect (in mm) (OR = 1.016; 95% CI: 1.004–1.028; p = 0.009) as independent risk factors associated with graft complications with high accuracy of prediction (AUC = 0.815). Intensive care (OR = 4.419; 95% CI: 1.576–12.388; p = 0.005) with a coefficient between intensive care and OPD (0.214) being low was identified as the most relevant risk factor for infection. Although intensive care is not a classic risk factor, but rather a summation of factors not reaching significance in the individual case, a stay in ICU (intensive care unit) needs to be considered for graft complications. As a clinical consequence, we recommend using the best possible hygienic measures during procedures e.g., while performing dressing and drainage changes in ICU.