Bio-based liquid energy carriers have attracted great interest in research and industry due to their high energy densities and similarity to fossil fuels in terms of combustion, storage and distribution. Furthermore, they are aimed to reduce atmospheric carbon dioxide accumulation and the dependence on depleting fossil resources. Thinking beyond first and second generation biofuels, the tailoring of novel fuel structures obtained either from syngas (CO/H2) or from direct refunctionalization of monomers derived from biomass offers the opportunity to design fuels which exhibit optimal properties with respect to application and production. Facing the challenge of computer-aided identification of such advanced biofuels manufactured in efficient processes, the present contribution reviews the model-based product and process design approaches in chemical engineering and shows how these methodologies can be adapted, integrated and extended towards the design of entire value chains for novel biofuels.