Our increasing demand for materials and energy has put critical roadblocks on our path towards a sustainable society. To remove these roadblocks, it is important to engage in smart research and development (R&D). We present an early-stage sustainability assessment framework that is used to analyze eight new bio-based process alternatives developed within the CatchBio research consortium in the Netherlands. This assessment relies on a multi-criteria approach, integrating the performance of chemical conversions based on five indicators into an index value. These indicators encompass economics, environmental impact, hazards and risks thereby incorporating elements of green chemistry principles, and techno-economic and life cycle assessments. The analyzed bio-based options target the production of fuels and chemicals through chemical catalysis. For each bio-based process, two R&D stages (current laboratory and expected future) are assessed against a comparable conventional process. The multi-criteria assessment in combination with the uncertainty and scenario analysis shows that the chemical production processes using biomass as feedstock can provide potential sustainability benefits over conventional alternatives. However, further development is necessary to realize the potential benefits from biomass gasification and pyrolysis processes for fuel production. This early stage assessment is intended as an input for R&D decision making to support optimal allocation and utilization of resources to further develop promising bio-based processes.