This study aimed to describe the clinical presentation, microbiological profile and management of complications of bone wax usage for surgical procedures at the skull base. The case records of a series of five patients who developed post-operative surgical site complications because of bone wax usage during skull base surgery were reviewed. In all five patients, persistent site-specific clinical features were noted along with intra-operative presence of excessive bone wax. Three unique cases of presentation, one with a fungal brain abscess because of Aspergillus flavus infection, another with fungal osteomyelitis because of Trichosporon beigelii infection and a third with intradural migration of bone wax into the cerebellopontine angle cistern are highlighted. The presentation of surgical site infection at the skull base because of excessive use of bone wax can be manifold. The need for testing appropriate cultures including fungal culture is highlighted.