We develop a superstructure framework for the design of biorefineries for ethanol upgrading into advanced biofuels to replace gasoline, jet fuel or diesel. The framework integrates catalysis, process synthesis, and fuel property modelling towards the design of biorefineries producing fuels with specified properties. The proposed framework is applied to identify strategies for the upgrading of ethanol into one or more fuels with specific properties. We discuss the trade-off between profit and biorefinery complexity, as well as the relation among fuel property constraints, the optimal upgrading strategy selected, and process economics. Lastly, we show how to find the optimal biorefinery associated with a particular chemistry or catalyst. The results presented constitute the first systematic study of ethanol upgrading considering, simultaneously, fuel and process design.