There are concerns that general dentists (GDs) and dental specialists may be prescribing antibiotics inappropriately. This study explored the prescribing habits and decision-making processes of GDs versus oral and maxillofacial surgeons (OMFSs). A case-based online questionnaire was used to examine the prescribing of therapeutic and prophylactic antibiotics in two clinical scenarios. Stratified and systematic sampling strategies were implemented to provide a representative sample. The final valid sample was 60 GDs and 18 OMFSs. The majority of OMFSs (61.1%) routinely prescribed antibiotics for the surgical removal of third molars, which was significantly greater than for GDs (23.5%). For implant placement procedures, 72.2% of OMFSs and 62.1% of GDs prescribed antibiotics. Amoxicillin was the most selected agent for both scenarios. All OMFSs would prescribe antibiotic prophylaxis for patients with uncontrolled diabetes mellitus in both cases, but only 56.0–63.0% of GDs would do this. GDs based prescribing decisions primarily on information from prescribing guides, while OMFSs relied more on information gained from specialist training. Surgical prophylaxis protocols differed considerably between groups. Both groups used surgical prophylaxis for some situations that are outside current recommendations. Education with regards to discrepancies between clinical practice and current guidelines for antimicrobial therapy is needed to progress antimicrobial stewardship.