Purpose: Palm oil systems generate substantial amounts of biomass residues which are, according to best agricultural practices, preferably returned back to plantation in order to maintain soil fertility. However, there are often variations in this practice. Differences in economic status and possible treatment options for biomass residues determine the preferences to perform life cycle assessment (LCA), leading to a divergence in results. Difficulties when comparing LCA results based on literature are not unusual. The objectives of this paper are to provide guidelines for methodological choices that enable a systematic comparison of diverse scenarios for the treatment and valuation of empty fruit bunches (EFBs) and to explore effects of the scenarios on the environmental performances of a palm oil system.Methods: Eleven scenarios were selected to address the possible EFB valuation and expanded boundaries with reference to the main palm oil system (EFBs applied as mulch, converted to compost or ethanol, treated in an incinerator, and sold as coproducts). The life cycle inventories were modeled based upon an Ecoinvent database. Solutions to multifunctional problems were suggested, including the application of system expansion, substitution, and partitioning, depending upon the nature of the scenarios.Results and discussion: Comparison among LCA results based on the same multifunctional units (crude palm oil + palm kernel oil + palm kernel cake) can be accomplished only in cases where additional coproducts were utilized internally. Based on the global warming impact, the mulch option was preferred. The effect of the avoided process of producing synthetic fertilizers and the assumption that all parts of mulch are available as soil nutrient dominantly determined the final result. These need further verification. This study also demonstrates that the status of EFB as waste or goods is influential on the final results if the EFB is employed externally but has no effect if it is utilized internally.Conclusions: The proposed guidelines provide methodological choices in terms of system boundary, functional unit, and solutions to multifunctional problems. The methods can be used to systematically compare LCA results of different treatment options and valuation of EFB. The preferred alternative for managing this biomass residue could improve environmental performances and orient toward best practices, such as those suggested by the Roundtable on Sustainable Palm Oil (RSPO). Further studies incorporating a site-specific case of palm oil systems would better illustrate the usefulness of the proposed guidelines.