Generating bioenergy is a significant challenge in reducing the environmental impact of fossil fuel combustion and in sustaining energy and energy independence. This study focuses on the production of biofuel from lignocellulosic resources by the action of yeast or bacteria, whereas algae are excluded as a source of biofuels. Ethanol, lipids (as precursors to biodiesel and biojet fuel), and hydrogen are considered in this study. Different pretreatments for converting lignocellulose into liquid and gaseous carbon sources for the microbial production of biofuels are summarized, and their current and future prospects are discussed. This study highlights the scientific and technological limitations of producing biofuel from lignocellulosic substrates with low initial carbon content, generating inhibitors during pretreatments, limiting mass transfer of gas to liquid, and obtaining low yields of products converted from carbon. Studies are improgress to combine new engineered strains with innovative integrated bioprocesses, which can open up new opportunities. The refinery method effectively combines high-added-value chemical and energetic applications by optimizing by-product valorization and recycling. This method can reinforce both the economic and environmental viability of the lignocellulosic biofuel pathway. (C) 2016 Elsevier Ltd. All rights reserved.