An integrated biorefinery is a processing facility that integrates multiple biomass conversion pathways to produce value-added products. To date, various biomass conversion pathways are available to convert biomass into a wide range of products. Hence, there is a need for a methodology capable of evaluating the integrated processes in order to identify the optimal products possible to be produced from biomass and the optimal conversion pathway in producing them. In many cases where the desired properties cannot be met by a single molecule, an optimal mixture of chemicals would be required. In this respect, product and process design decisions would be a challenging task for an integrated biorefinery. In this work, a two-stage optimisation approach is developed to identify the optimal conversion pathways in an integrated biorefinery which convert biomass into an optimal mixture with desired properties. In the first stage, the optimal mixture is designed via computer aided molecular/mixture design (CAMD) tools. Once the optimal mixture is established, the second stage determines the optimal conversion pathway via superstructural mathematical optimisation approach. With such approach, the optimal conversion pathway can be determined based on different optimisation objectives. To illustrate the proposed methodology, a case study on the design of fuel additives as a mixture of different molecules from palm-based biomass is presented.