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Abstract The bioeconomy is a shared vision for a future European industry entirely based on organic matter. Authorities support this technological development with subsidies and policies stimulating R&D. One major limitation for the bioeconomy is that R&D and industrial growth require the continuous availability of biomass as a primary resource. This resource dependence is already present during the formative years of new biobased innovations and influences the pilot and demonstration phase of the development. Traditionally, it is assumed that public support for pilot and demonstration initiatives may overcome this hurdle. In this paper, we investigate how this resource constraint limits the effectiveness of bioeconomy policies. The future development of the biobased sector is simulated including the inherent dependence of industrial activity on biomass. We simulate the future growth and technological diversity of an emerging biotechnological sector: the sector of manure transformation in Belgium. The paper reports the evolutions for three policy scenarios. The model explicitly accounts for endogenous innovation and knowledge transfer mechanisms. The results show that policies may have an important impact on the sector structure in the long run, but the sector growth remains ultimately constrained by the availability of inputs. So bioeconomy policies to promote innovation will be less effective, unless mechanisms are included to alleviate the resource constraint. Highlights • Biomass resource constraints impact the effectiveness of bioeconomy policies. • Bioeconomy policies may have an important impact on the sector structure in the long run, but the sector growth remains ultimately constrained by the availability of inputs. • Solutions to reduce the biomass constraint have to be included in innovation policy for the biobased economy. [ABSTRACT FROM AUTHOR]