Recent political and economic developments have prompted Malaysia to seek for opportunities in implementing renewable energy generation projects to meet commitments pledged at the 21st Conference of Parties (COP21). Essentially, Malaysia pledged to reduce its carbon emissions intensity by 45% of its GDP in 2005. However, Malaysia would require further systematic planning for its renewable energy sector to achieve such pledge. To address this need, this chapter applies a hybrid methodology to systematically plan and optimize a bioenergy supply chain (BSC) in Malaysian palm oil industry. This methodology first uses carbon emission pinch analysis (CEPA) to determine the minimum renewable energy requirement based on a given carbon emission reduction target. Based on this minimum requirement, a BSC superstructure is optimized to establish the optimal routes in achieving the set emission reduction target. Results suggest that the optimized BSC with 4,644 TJ output could reduce CO2 emission intensity by 8.95%.