Tissue scarcity poses global challenges for corneal transplantation and public health. Xeno-keratoplasty using animal-derived tissues offers a potential solution, but its environmental and economic implications remain unclear. This study evaluated two xeno-keratoplasty procedures at a single institution: (1) native corneas (Option 1) and (2) tissue-engineered corneal scaffolds derived from slaughterhouse waste (Option 2). Life cycle assessment (LCA) quantified environmental impacts across 18 midpoint indicators, while cost-effectiveness analysis (CEA) incorporated cost and environmental impact using two approaches. Option 1 exhibited significantly lower environmental impact than Option 2 across most indicators, primarily due to the energy and equipment demands of cell culture in Option 2. Both CEA approaches (carbon offset pricing and utility decrement) demonstrated cost-effectiveness dominance for Option 1. Xeno-keratoplasty using native corneas (Option 1) appears more environmentally and economically favorable than tissue-engineered scaffolds (Option 2) in the current analysis. Future studies could explore diverse xeno-keratoplasty techniques for optimizing sustainability.