The replacement of fossil resources with renewable biomass in a bioeconomy is seen as a major contribution to climate change mitigation. This transformation will affect all members of society, making it crucial to consider the views of different stakeholders to ensure a socially acceptable transition towards a sustainable bioeconomy. To explore potential outcomes of bioeconomy strategies assuming different future pathways, a scenario analysis is a tool to inform decision-makers about policy impacts and trade-offs. The inter- and transdisciplinary research project “BioNex – The future of the biomass nexus” is the first project to develop bioeconomy scenarios together with stakeholders from politics, industry, and civil society in an iterative co-design process. As a result, three storylines describing diverging potential global futures are developed and quantified: Towards sustainability, business as usual, and towards resource depletion. The futures are driven by different assumptions on climate policy, cropland expansion, productivity growth in agriculture, prices of fossil energy, and consumption behaviour. Additionally, in the co-design process, three bioeconomy policies are developed: policy as usual, stronger development of the bioeconomy, and no policies. Besides presenting the results of the stakeholder workshops, this paper evaluates the strengths and shortcomings of a stakeholder approach in terms of policy-oriented research. According to the experience made within this study, it provides valuable insights for researchers and funding authorities they can use to optimise the employment of stakeholder-based research approaches.