Sector-specific strategies are needed to transition toward a low-carbon economy. Palm oil is a large-scale agriculture commodity in Malaysia, with a considerable carbon footprint. Therefore, decarbonization of the palm oil sector is crucial, accounting for emissions and mitigation opportunities along the entire value chain. Though several of the previous works have optimized the palm oil value chain (POVC), there exists a significant gap in the comprehensive evaluation of strategies to decarbonize the POVC. To address this gap, this work proposes a systematic approach to design an optimal POVC with minimum GHG emissions. This study considers integrated oil palm plantations (OPPs), integrated palm oil mills (POMs), and palm oil refineries (PORs) within the POVC boundary. An integrated OPP refers to plantation with an onsite biorefinery, while an integrated POM includes the milling process, biorefinery, palm oil mill effluent (POME) treatment, and biogas upgradation. A mathematical optimization (mixed integer nonlinear programming, MINLP) model was developed to determine the optimal process design and pathway selection along the POVC. The proposed model is illustrated with a case study of POVC in Johor, Malaysia that includes 15 OPPs, 5 POMs, and 1 POR. The optimization was performed under two scenarios�maximizing economic performance (S1) and maximizing GHG savings (S2). The results of this study show a significant improvement in the annual economic performance from USD 85 million in the existing baseline scenario to USD 167 million in S1. Furthermore, the study demonstrates that optimal technology and pathway selection can result in significant GHG savings up to 6.04 tCO 2 /ha at OPPs and 0.62 tCO 2 /t FFB at POMs, respectively.