There is no established consensus or standardized method for the preparation of amniotic membrane extract (AME). Consequently, various preparation, preservation, and sterilization techniques have been employed. To obtain AME rich in bioactive components with high therapeutic efficacy, each step of the preparation process is of critical importance. The appropriate procurement of the amniotic membrane minimizes the risk of infection transmission and reduces inter- and intra-donor variability. For the subsequent extraction process, different approaches are utilized due to factors such as laboratory infrastructure variability and the lack of a standardized method. Although lyophilization has recently emerged as a prominent method for the long-term preservation of AME, further investigation is required to assess its impact on the biochemical composition and clinical efficacy of the membrane. In ophthalmology, in vitro, in vivo, and clinical studies indicate that AME supports corneal epithelial regeneration, suppresses inflammation, and is a well-tolerated therapeutic agent. Consequently, further studies are still needed to enhance the effective release of therapeutic components from the amniotic membrane, improve the quality and consistency of AME, and preserve its content over an extended period. Thus, the clinical application of AME-derived products in the form of eye drops will become more widespread in the future.