The production of renewable energy has become a priority in the European Union given the depletion of fossil fuels and the deterioration of the environment. Waste and specifically biowaste, the organic fraction of municipal solid waste, is considered as an ideal raw material for the production of bioethanol. However, bioethanol production from biowaste in large scale is a complex project that requires the participation and the engagement of different stakeholders that are involved in the different steps of the process from the collection of the waste to the production of the final product and the management of the residues. Fuzzy Cognitive Maps, a soft computing technique for analyzing complex decision-making problems, is applied to identify the critical factors that will affect the large-scale production of bioethanol from biowaste. Results indicate that the different groups of stakeholders have a different perception and identify different factors as the driving forces of the project. The effect of political, social and technoeconomic factors on the overall success of the project has been examined. Simulations have shown that the model developed is mainly sensitive to the political factors involved.