There is an increasing trend in promoting the use of biofuels for transportation as a low-fossil carbon energy source, but little knowledge on their multidimensional environmental impacts. Whole-system approaches, such as life cycle assessment (LCA), have been extensively employed to analyze the environmental performance of different biofuels. However, it remains unclear to which extent biofuels impact ecosystems and the services they provide, in particular related to different management practices. To overcome this challenge, this paper draws recommendations to better holistically address ecosystem services (ES) in LCA, with a focus on biofuels. We first pinpoint some of the challenges in accounting for the concept of ES in decision-making and review some of the existing ES classification frameworks and the usefulness of the cascade model. Second, we discuss the implications of identified context-specific aspects on the modeling of biofuel production impacts on ES in LCA. Finally, we propose a conceptual framework to link ES classification systems, the cascade model and the LCA approach. Although some challenges still remain unsolved, due to the existing life cycle impact assessment structure, existing ES frameworks and the cascade model are helpful tools to better include ES into LCA of different biofuels.