Background/Objectives <p>Amniotic membrane transplant (AMT) is used in the management of persistent epithelial defects (PED). We used cryopreserved (CAM) and vacuum dried (Omnigen) amniotic membranes to treat PED and studied the changes in the membranes and cornea during healing.</p> Subjects/Methods <p>ASOCT scans were obtained from 29 consecutive patients with PED. Fourteen eyes underwent cryopreserved amniotic membrane transplant (CAMT) and 15 underwent Omnigen transplants. ASOCT was done before the surgery and at 1 week and at 3–4 weeks. Heidelberg calliper was used to measure thickness of the epithelium, amnion, stromal bed and total cornea. Healing of PED was monitored by fluorescein staining and slitlamp examination. Success was defined as complete epithelialisation of the PED. Unsuccessful eyes were excluded from analysis. Statistics was performed using GraphPad Prism 8.2.1. P value of less than .05 was considered significant.</p> Results <p>Healing of PED was seen in 75.86% (<i>n</i> = 22) of eyes. Eyes treated with CAMT and Omnigen showed a significant reduction in stromal bed thickness between the initial presentation and the healed stage (<i>p</i> = 0.025 and 0.017, respectively,) but there was no significant inter-membrane difference. There was no significant difference between the thickness measurements ascertained for the other parameters mentioned above.</p> Conclusion <p>This study demonstrates that both CAM and Omnigen give similar results for healing of PED, and thickness of the epithelium, amnion, residual stroma and total cornea suggesting that they are equally effective in the management of PED. ASOCT can provide quantitative information on the healing of PED with AMT.</p>