The transition to a bio-based economy is expected to deliver substantial environmental and economic benefits. However, bio-based production systems still come with significant environmental challenges, and there is a need for assessment methods that are adapted for the specific characteristics of these systems. In this review, we investigated how the environmental aspects of bio-based production systems differ from those of non-renewable systems, what requirements these differences impose when assessing their sustainability, and to what extent mainstream assessment methods fulfil these requirements. One unique characteristic of bio-based production is the need to maintain the regenerative capacity of the system. The necessary conditions for maintaining regenerative capacity are often provided through direct or indirect interactions between the production system and surrounding "supporting" systems. Thus, in the environmental assessment, impact categories affected in both the primary production system and the supporting systems need to be included, and impact models tailored to the specific context of the study should be used. Development in this direction requires efforts to broaden the system boundaries of conventional environmental assessments, to increase the level of spatial and temporal differentiation, and to improve our understanding of how local uniqueness and temporal dynamics affect the performance of the investigated system.