Diversifying energy through alternative sources, such as biofuels, is a practical and accessible option in Indonesia. This study aimed to optimize the yield of biofuel (green diesel) using Ni/marble waste as a catalyst. Deoxygenation offers a promising route for converting waste cooking oil (WCO) into valuable products. A Box–Behnken Design (BBD) was applied to assess the effects of key variables on the deoxygenation process using Response Surface Methodology (RSM). The variables included reaction time (2–6 h), reaction temperature (360–380 °C), and catalyst weight (1–3% w/w), with conversion percentage as the response. The results showed that reaction time and catalyst weight significantly influenced WCO deoxygenation (p < 0.05). The optimum conditions for maximum conversion were a reaction temperature of 373.64 °C, a catalyst weight of 3.45% w/w, and a reaction time of 4.35 h. Under these conditions, hydrocarbon selectivity reached 92.26%. Paraffins were the dominant fraction, confirming that the Ni/marble catalyst efficiently promoted deoxygenation with high selectivity toward C15–C18 hydrocarbons. These findings align with the proposed reaction mechanism, which involves decarboxylation, decarbonylation, and hydrodeoxygenation pathways. An economic evaluation under optimal conditions estimated a profit of $1.0469 per batch, demonstrating that converting waste cooking oil into green diesel is both technically feasible and economically attractive. Overall, integrating waste-derived catalysts with optimized deoxygenation technology provides a sustainable and profitable solution.