Increasing the use of renewable energy sources is one of the most important goals of energy policies in several countries to build a sustainable energy future. This contribution proposes the synthesis of a biorefinery supply network for a case study of the European Union (EU-27) under several scenarios based on a mathematical programming approach. Several biomass and waste sources, such as grains, waste oils, and lignocellulosics, are proposed to be utilized, and various biofuels including first, second, and third generations are produced such as bioethanol, green gasoline, biodiesel, Fischer Tropsch (FT) diesel, and hydrogen. The aim of this study is to evaluate the capabilities of EU-27 countries to be able to meet the Renewable Energy Directive (RED II) target regarding the share of renewable energy in the transport sector by 2030 in each Member State while not compromising the current production of food. A generic mathematical model has been developed for the multi-period optimization of a biorefinery supply network with the objective of maximizing sustainability profit. The solutions obtained show that biomass and waste are promising raw materials to reach and go beyond the EU’s renewable energy target in the transport sector for the year 2030. However, some countries would need to provide additional subsidies for their companies to achieve at least a non-negative economic performance of biofuel production.