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Purpose The purpose of this study was to assess cryopreserved amniotic membrane (C-AM) versus chorion-free freeze-dried amniotic membrane (FD-AM) overlay transplantation for corneal ulcers in a French tertiary ophthalmology hospital. Methods Between March and July 2020, when C-AMs were not available because of the COVID-19 pandemic, 28 corneal ulcers underwent FD-AM overlay transplantation and were retrospectively compared with 22 corneal ulcers treated with C-AM during the same period in 2018. All patients had at least 3 months of follow-up, and those who underwent combined surgeries were excluded. Ulcers were assessed at baseline and then at 72 hours, 1 month, and 3 months. Population demographics, follow-up time, ulcer etiologies, epithelial defect size, ulcer depth, and complications were also recorded. Results Baseline characteristics and clinical features of both groups were comparable. There was no statistically significant difference in the number of overlay AM transplantations (P = 0.52) or early detachments (P = 0.57). At 3 months, the corneal healing rate was almost the same in both groups (89% and 91% for FD-AM and C-AM, respectively; P = 0.87). Complications were equally uncommon (11% and 9%, respectively; P = 0.92). In logistic regression, the type of the membrane did not influence corneal healing at 1 month (P = 0.42) or 3 months (P = 0.99), regardless of the depth of the ulcer. However, whatever the type of AM used, the deeper the ulcer was, the less likely it was to heal at 3 months (P = 0.02). Conclusions This is the first study that provides positive insight into the effectiveness of FD-AM compared with C-AM when used as overlay transplantation for treating corneal ulcers.