The goal of this study was to review the incidence, risk factors and outcomes of microbial keratitis after penetrating keratoplasty (PK) and endothelial keratoplasty (EK). Methods: The electronic medical records at Wills Eye Hospital were queried for cases of microbial keratitis following PK or EK performed between 1 May 2007 and 1 September 2018. Charts were reviewed to obtain demographic data, transplant characteristics, details of microbial keratitis, graft survival and clinical outcomes. Results: During the study period, 2098 transplants were performed in 1601 patients. Of these, 1267 (60.4%) were PKs and 831 (39.6%) were EKs. We identified 86 (4.1%) cases of subsequent microbial keratitis. The incidence of microbial keratitis after PK was significantly higher than after EK (5.9% versus 1.3%; p = 0.005). Furthermore, the rate of infection was higher after repeat transplants (either PK or EK) compared to initial keratoplasties (5.5% versus 3.4%; p = 0.02). Twenty-six (32.1%) grafts remained clear at most recent follow-up after microbial keratitis, and the proportion of clear grafts was higher after EK than PK (66.7% versus 27.8%; p = 0.03). Conclusion: Rates of microbial keratitis were significantly higher after PK compared to EK, and repeat transplantation was a risk factor for microbial keratitis. To the best of our knowledge, there is no prior study in the literature evaluating microbial keratitis rates after PK and EK and comparing outcomes.