Palm oil systems generate large amounts of biomass residues. According to best agri-cultural practices, they are supposed to be returned back to plantation to maintain soil fertility. However, there are variations in practice. Differences in economic status and treatment options on biomass residues cause variations on the preference to perform LCA, leading to divergence in results that complicate interpretation. Difficulties found in comparing LCA results based on literature are not unusual. The objective of the paper is to provide guidelines on methodological choices to systematically compare diverse sce-narios on the treatment and valuation of EFB (Empty Fruit Bunches) and to explore their effects on the environmental performances of a palm oil system. Eleven scenarios were chosen to cover possible EFB valuation and expanded system boundaries with reference to the main palm oil system (application as mulch, conversion to compost or ethanol, treatment in an incinerator, and EFB as direct co-products). The life cycle inventories were modeled based on Ecoinvent database. The input EFB was considered either as wastes or goods, and the resulted products were used internally or externally. Solution to multi-functional problems was suggested, including the application of system expansion, substitution, and partitioning depending on the nature of the sce-nario. The contribution of the plantation phases on global warming impact was so dominant that the effect of different scenarios could be observed only when focusing on the oil mill stage. Comparison among LCA results based on the same multi-functional units (crude palm oil + palm kernel oil + palm kernel cake) can be done only in the cases where addi-tional co-products (mulch, compost, or ethanol) were used internally. Based on global warming impact, the mulch option was the best choice as compared to the compost, eth-anol, or incineration options. The effect of the avoided process of producing substituted fertilizers wa