Advanced oxidation processes (AOPs) are powerful methods that were traditionally used for treatment of hazardous materials. Based on their resourcefulness, these methods have recently found important applications in various processes of bioenergy production. Despite the growing interest in the application of AOPs in improving the production of bioenergy, there is no comprehensive documentation on how biofuels production operations have increasingly incorporated these oxidation processes. Therefore, the present study aims at reviewing the current state of the art and future prospects of applying AOPs in biofuels production. The usage of these processes in pre-treatment of lignocellulosic biomass, excess sludge, organic effluents, solid wastes and other substrates for energy production was reviewed. It was noted that wet air oxidation has high potential in pretreatment of lignocellulosic biomass for production of various energy types while sonolysis is most effective in biosolids pretreatment. Ozonolysis and photocatalysis are mostly used to selectively remove the colorants in organic effluents. However electrochemical oxidation has good performance in post-treatment of bioenergy effluents. Documented studies indicate that AOPs can be used to enhance trans-esterification thereby boosting biodiesel production. Moreover, they can be used to improve oil extraction from bio-algae to increase biodiesel yields. Comparative studies involving AOPs and conventional processes are necessary to determine their suitability for these applications. The possibility of using AOPs to upgrade low value biofuels to bio-products of higher value should be part of future investigations. A summarized criterion for evaluating the suitability of different AOPs in the production of biofuels is proposed in this study as a guide for their future usage. The main limitation of applying AOPs in bioenergy sector include high process costs due to costly chemicals and energy requirements. Further studies should investigate the possibility of integration of AOPs with conventional methods aimed at improving the process cost-effectiveness.