Background: Surgical site infections (SSIs) remain a major source of morbidity after pancreatoduodenectomy (PD). We noted a higher than anticipated incidence of SSI in our patients undergoing PD, and after an internal audit and detailed analysis of the microflora of SSIs, as well as a multidisciplinary discussion, the local prophylactic antibiotic policy was changed based on sensitivities to the bacteria isolated from post-operative infections. The hypothesis was that a targeted change in antibiotic prophylaxis would reduce the rate of SSIs. The aim of the current study was to analyze the results of a change in prescribing policy on SSI rates, and in addition, on the occurrence and severity of post-operative pancreatic fistulae (POPF) because this complication is often linked to the presence of an organ/space SSI. Methods: After implementing a change of prophylaxis policy from cefalexin to ceftriaxone and metronidazole, and educating staff and residents, a prospectively maintained departmental database was used to identify consecutive patients undergoing PD pre-and post-institution of policy change. Incidence data relating to SSIs and POPF were obtained from the American College of Surgeons-National Surgical Quality Improvement Program (ACS-NSQIP) data set and the details of culture results and organism sensitivity extracted from the electronic medical record, as were details on the severity of fistulae, and verified by the senior author. Results: The pre-and post-implementation cohorts consisted of 111 and 216 patients, respectively, and were matched in terms of all demographic features. After the change in the antibiotic prophylaxis policy, there was a reduction in the overall SSI rate (26.4% vs. 14.8%; p = 0.01) and the organ/space SSI rate (OS-SSI; 15.3% vs. 8.6%; p = 0.03). There were also reductions in the POPF rate (38.2% vs. 19%; p = 0.002) and in the clinically relevant POPF (CR-POPF; 23.4% vs. 6.0%; p = 0.001). The rate of Clostridium difficile infections also decreased (8.1% vs.1.9%; p = 0.006) as did the median length of hospital stay (7 vs. 6 days; p = 0.003). After excluding patients with a penicillin allergy (n = 24) from the post-implementation cohort, cases compliant (158/ 192) and non-compliant (34/192) to the new antibiotic policy were compared. The overall SSI (26.4% vs. 10.7%; p = 0.025), OS-SSI (17.6% vs. 5.1%; p = 0.021), overall POPF (32.4 vs. 14.6; p = 0.023); CR-POPF (10.8% vs. 5.5%; p = 0.047) and Clostridium difficile (8.8% vs. 1.3%; p = 0.040) were all lower in the compliant patient cohort. Conclusions: A change in antibiotic prophylaxis prior to PD based on the local microflora, resulted in reductions in SSI, POPF, and Clostridium difficile rates.