This study presents a cradle-to-gate assessment of the energy balances and greenhouse gas (GHG) emissions of Indonesian palm oil biodiesel production, including the stages of land-use change (LUC), agricultural phase, transportation, milling, biodiesel processing, and comparing the results from different farming systems, including company plantations and smallholder plantations (either out growers or independent growers) in different locations in Kalimantan and Sumatra of Indonesia. The findings demonstrate that there are considerable differences between the farming systems and the locations in net energy yields (43.6–49.2 GJ t−1 biodiesel yr−1) as well as GHG emissions (1969.6–5626.4 kg CO2eq t−1 biodiesel yr−1). The output to input ratios are positive in all cases. The largest GHG emissions result from LUC effects, followed by the transesterification, fertilizer production, agricultural production processes, milling, and transportation. Ecosystem carbon payback times range from 11 to 42 years.