Policymakers worldwide are promoting the use of bio-based products as part of sustainable development. Nonetheless, there are concerns that the bio-based economy may undermine the sustainability of the transition, e.g., from the overexploitation of biomass resources and indirect impacts of land use. Adequate assessment methods with a broad systems perspective are thus required in order to ensure a transition to a sustainable, bio-based economy. We review the scientifically published life cycle studies of bio-based products in order to investigate the extent to which they include important sustainability indicators. To define which indicators are important, we refer to established frameworks for sustainability assessment, and include an Open Space workshop with academics and industrial experts. The results suggest that there is a discrepancy between the indicators that we found to be important, and the indicators that are frequently included in the studies. This indicates a need for the development and dissemination of improved methods in order to model several important environmental impacts, such as: water depletion, indirect land use change, and impacts on ecosystem quality and biological diversity. The small number of published social life cycle assessments (SLCAs) and life cycle sustainability assessments (LCSAs) indicate that these are still immature tools; as such, there is a need for improved methods and more case studies.