Fossil fuel reliance in the transportation sector remains a leading contributor to global greenhouse gas emissions, underscoring the urgent need for renewable alternatives like biodiesel. Derived from renewable feedstocks, biodiesel can reduce emissions, enhance energy independence, and support rural economies. However, its production faces challenges such as low energy efficiency, process optimization barriers, and the limited utilization of byproducts like glycerol, which elevate costs and hinder large-scale adoption. This study addresses these challenges by developing an integrated framework for biodiesel production and byproduct valorization, supporting the long-term decarbonization of biofuel production. Three key feedstocks�refined palm oil, rapeseed oil, and soybean oil�are evaluated for biodiesel yield. The single-step transesterification process is enhanced through a two-stage approach, optimizing fatty acid methyl ester conversion under varying methanol and NaOH catalyst split ratios. Glycerol valorization strategies, including combustion, purification, and anaerobic digestion, are analyzed to improve economic and environmental sustainability. Using mixed-integer linear programming (MILP), the study minimizes total costs by balancing operational and capital expenditures while incorporating process integration constraints. The findings provide actionable insights into cost-effective and sustainable biodiesel production pathways, promoting the broader adoption of biofuels in the transition toward net-zero emissions.