Microsurgery is the gold standard for hard and soft tissue reconstruction in head and neck neoplasia and malformations. Fibular, iliac crest, and scapular free flaps are the main choices for reconstructive surgery of the jaws. Although widely described in the literature, no statistical comparison analysis of the donor site morbidity of these has been performed to our knowledge. Therefore, in this study, the medical records of patients who underwent microsurgical jaw reconstruction at the Maxillofacial Oncological Reconstructive Surgery Unit of Umberto I General Hospital in Rome between 2011 and 2021 were analysed retrospectively. Inclusion criteria were complete clinical and radiological records, microsurgical reconstruction harvesting one of the three flaps, and a minimum follow up of 12 months. Principal donor site complications were recorded and compared among the flaps. The data were analysed using IBM SPSS Statistics (28.0.1.1, IBM Corp). The study enrolled 220 patients: 103 with deep circumflex iliac artery (DCIA) flaps, 87 with fibular free flaps (FFF), and 30 with scapular bone flaps (SBF). The main DCIA donor site complications were dysaesthesia (13.6%), abdominal hernia (2.9%), dehiscence (1.9%), infection (1.9%), and anterior superior iliac spinal fracture (1.9%). Similarly, the main FFF complications were dehiscence (8%), skin graft necrosis (6.9%), infection (5.7%), and dysaesthesia (3.4%). Subcutaneous seroma occurred in 13.3% of SBF patients and dehiscence in 6.7%. Regional dysaesthesia occurred significantly (p < 0.05) more often in DCIA than FFF or SBF patients. Dehiscence was significantly (p < 0.05) more frequent in FFF than DCIA or SBF patients. All flaps were safe and associated with low donor site morbidity. The jaws should be reconstructed selecting the flap that best satisfies the reconstructive needs based on the patient’s clinical features.