To assess the risk factors and management of corneal plaques formed after keratoplasty. In this retrospective study, medical records of all eyes with plaques formed on top of corneal grafts performed in the period between January 2014 and January 2022 were reviewed. The retrieved data included prekeratoplasty corneal pathology, ocular risk factors, operative data and complications, plaque management, and chemical composition of the plaques using infrared spectrometer. Thirteen eyes were included in this study. Predisposing ocular comorbidities included ocular surface disorders with variable degrees of dry eye in nine patients, rheumatoid arthritis in three patients, history of herpetic keratitis in two eyes, and cicatrizing conjunctivitis in two patients. Surgical excision and amniotic membrane transplantation (AMT) were performed in 12 eyes. Postoperatively, five eyes showed recurrence after excision, two eyes developed graft vascularization and scarring, and one eye showed persistent epithelial defect and graft scarring, whereas four eyes showed complete epithelialization with mild haze. Rekeratoplasty and AMT were performed in two eyes with no plaque recurrence. Chemical analysis using infrared spectrometry showed that the plaques consisted of ammonium magnesium phosphate and calcium phosphate carbonate in 9 (75%) cases and pure mucus in 3 (25%) cases. Postkeratoplasty corneal plaque formation is an underestimated complication of keratoplasty that may occur after persistent epithelial defects. Ocular surface disorders are the primary predisposing risk factors. In our experience, the prognosis after medical treatment or surgical scraping is guarded, and regrafting can be the only solution to restore graft clarity.