The distribution of bio-based diesel fuel commodities in Indonesia faces efficiency challenges due to fluctuating demand, geographically dispersed delivery points, and mismatches between shipment volumes and vessel capacities. Since maritime transport is a dominant mode in the national distribution network, optimizing sea-based logistics is crucial to reducing costs and ensuring reliable energy supply chains. This study addresses these challenges by focusing on maritime transportation and utilizing real-world allocation data from 2024 in Indonesia, consisting of 22 origin points and 51 destination points, with a total shipment volume of 9 million kiloliters. A monthly planning model based on recurring demand patterns is developed to design routes and number of deliveries, leveraging empirical data and addressing a real-world national logistics issue. A trip-based cost optimization model tailored to maritime logistics is employed to evaluate the effects of vessel suitability, consolidation strategies, and demand variability on delivery efficiency. This study shows that aligning vessel capacities with shipment volumes significantly reduces transportation costs, and implementing split deliveries when full consolidation is insufficient to meet monthly demand further enhances flexibility. Moreover, optimizing multi-destination routing combined with dynamic vessel selection and split delivery yields notable efficiency gains, achieving an overall cost reduction of more than 18% compared to the traditional point-to-point model. These findings highlight that consolidation, optimal vessel assignment and flexible split delivery can significantly enhance transportation efficiency. Finally, this study offers insights to improve the cost-efficiency of Indonesia’s bio-based diesel fuel that contributes to the reliability of its energy delivery systems.