Milkfish (Chanos chanos) is an abundant fish commodity in the Philippines that generates a large number of wastes such as skin, scales, viscera, and bones, which, upon disposal, cause environmental pollution. The abundance of these wastes, such as fish skin, rich in bioactive natural products such as collagen, elicits interest in their conversion into high-market-value products. The decellularization of milkfish skin waste can extract its extracellular matrix (ECM), a potential raw material for biomedical applications such as the repair of damaged skin tissues. In particular, this study characterized the developed decellularized ECM with different concentrations (0.1%, 1.0%) of the decellularizing agents (Triton X-100, SDS) and temperature (4 °C, room temperature) using milkfish skin. The decellularized ECM structure was better preserved using Triton X-100, while SDS was more effective in cell component removal, especially at 1% concentration and 4 °C temperature. There were significant effects of varying the temperatures and concentrations on the physical and mechanical properties of the decellularized ECM. Future studies could explore more variables to further establish protocols and more analyses to better characterize the decellularized milkfish skin.