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The expansion of the bioeconomy sector will increase the competition for agricultural land regarding biomass production. Furthermore, the particular path of the expansion of the bioeconomy is associated with great uncertainty due to the early stage of technology development and its dependency on political framework conditions. Economic models are suitable tools to identify trade-offs in agricultural production and address the high uncertainty of the bioeconomy expansion. We present results from the farm model Economic Farm Emission Model of four bioeconomy scenarios in order to evaluate impacts and trade-offs of different potential bioeconomy developments and the corresponding uncertainty at regional and farm level in Baden-Wuerttemberg, Germany. The demand-side effects of the bioeconomy scenarios are based on downscaling European Union level results of a separate model linkage between an agricultural sector and an energy sector model. The general model results show that the expanded use of agricultural land for the bioeconomy sector, especially for the cultivation of perennial biomass crops (PBC), reduces biomass production for established value chains, especially for food and feed. The results also show differences between regions and farm types in Baden-Wuerttemberg. Fertile arable regions and arable farms profit more from the expanded use of biomass in the bioeconomy than farms that focus on cattle farming. Latter farms use the arable land to produce feed for the cattle, whereas arable farms can expand feedstock production for new value chains. Additionally, less intensive production systems like extensive grassland suffer from economic losses, whereas the competition in fertile regions further increases. Hence, if the extensive production systems are to be preserved, appropriate subsidies must be provided. This emphasizes the relevance of downscaling aggregated model results to higher spatial resolution, even as far as to the decision maker (farm), to identify possible contradicting effects of the bioeconomy as well as policy implications.