Biofuels are a new emerging sector that attempts to evolve into a novel energy industry that would provide a sustainable future. For this reason, there is a need to find ways to make the production of biofuels economically feasible, in order to establish the biofuel industry. On the other hand, biphasic catalysis has already proved itself as an effective alternative to conventional catalytic methods. As a result, in the past few years there were attempts to use biphasic catalytic systems for the production of biofuel precursors, biofuel production and biofuel upgrading. Some of these efforts led to positive results, which are evidence that biphasic systems could have effective applications in the bioenergy. In the current book chapter, several biphasic catalytic systems applied in the biofuel sector were presented and discussed.