This is a monocentric, retrospective study of patients who underwent successful immediate or delayed maxilla or mandible reconstructions with FFF from January 2005 to December 2021. Panoramic radiograph, computed tomography scans, and cone-beam CTs were analyzed concerning the osseous union of the intersegmental junctions between maxillary or mandibular native jaw and fibular bone. The primary parameter was to estimate the status of osseous union according to osteosynthesis type. A total number of 133 patients (PSI: n = 64, non-PSI: n = 69) were included in the present study. The mean age was 56.7 ± 14.0 (Range: 14.7–82.7); the primary diagnosis was in 105 patients a malignant (78.9%) and in 20 patients a benign (15.0%) tumor. Mandible reconstruction was performed on 103 patients (77.4%), and on 30 patients (22.6%), maxilla reconstruction was performed. The radiographic images provided a rate of incomplete osseous union (IOU) of about 90% in both groups in the first 6 months. Imaging between 6 and 12 months reveals an IOU rate in the non-PSI group of 46.3% vs. 52.5% in the PSI group, between 12 and 24 months, an IOU rate of 19.6% vs. 26.1%, between 24 and 36 months 8.9% vs. 21.7%, and after 36 months the IOU rate decreases to 4.2% vs. 18.2%. Multivariate logistic regression shows that only osteosynthesis type (OR = 3.518 [95%-CI = 1.223–10.124], p = 0.02) and adjuvant radiotherapy (OR = 4.804 [95%-CI = 1.602–14.409], p = 0.005) are independent risk factors for incomplete osseous union. Cox regression revealed that the variables plate-system (Hazard ratio, HR = 5.014; 95 %-CI: 1.826–3.769; p = 0.002) and adjuvant radiotherapy (HR = 5.710; 95 %-CI: 2.066–15.787; p < 0.001) are predictors for incomplete osseous union. In our study, the rate of incomplete bony fusion was significantly higher in the PSI group. Jaw-to-fibula apposition zones were significantly more affected than intersegmental zones. In multivariate analysis, a combination of osteosynthesis with PSI and adjuvant radiotherapy could be identified as a risk constellation for incomplete ossification.