Abstract Purpose Carbon and biodiversity footprints are increasingly calculated. However, little attention has been paid to the coherency of methodological choices and interpretation of the footprint results. This paper aims to clarify the coherency between the choice of reference land use and carbon and biodiversity footprints and discuss the challenges encountered. Methods First, we analyse features of reference land use options proposed in ISO 14067 (2018) i.e. business as usual, projected future, target, potential natural regeneration and historic baseline. Second, we discuss the connection between temporal scope and life cycle of land use. Third, we provide guidance on how to choose reference land use coherently. Fourth, we discuss specific issues related to carbon and biodiversity footprints and their relationship to reference land use. Finally, we provide conclusions and recommendations for further conceptual development. Results and discussion Choice of reference land use and determination of temporal scope of a study may significantly influence the assessment of carbon or biodiversity footprints. If the aim of a footprint study is to assess the effects of land use, reference land use should describe dynamically non-use of land. Thus, potential natural regeneration or continuation of natural state (if it is the starting point) of land is the coherent reference land use in this case. If the aim of a footprint study is to assess the effects of a decision to change land use or its management, reference land use should describe dynamically alternative use of land expected without the studied decision. Business as usual or projected future is a coherent reference land use in this case. Historic baseline or target reference land use may be useful in comparing the ecosystem value of the studied land use with a pre-set historic baseline or (policy) target. Conclusions We conclude that coherent choice of reference land use for carbon or biodiversity footprints depends on the goal and scope of a study. Beyond methodological coherency, issues related to the reliability and availability of appropriate data are relevant and vary between reference land use choices. However, difficulties in the assessment should not justify incoherent choices. We recommend that uncertainties are not overlooked but incorporated in the assessment and considered in the interpretation of the results. In addition, we recommend that key methodological choices, including the definition of the purpose of a study, chosen temporal scope and applied reference land use, should be clearly and transparently presented.