<p>Microwaves offer volumetric heating with a higher energy efficiency than conductive–convective heat transfer in conventional approaches. The emerging application of microwave heating in biorefineries is a low-emission strategy to produce bio-based chemicals and materials. In this Review, we discuss the use of microwaves in biorefinery applications, including lignocellulose pretreatment, bioactive substance extraction, pyrolysis and hydrothermal treatment. Experimental evidence suggests that microwaves increase reaction rates, product yield and selectivity; however, these outcomes do not always occur. It is important that microwave-assisted techniques are assessed under controlled conditions to allow a fair comparison with conventional processing. Microwaves can induce hotspots in heterogeneous, multiphasic systems, which have reaction-specific impacts on the chemistry of the system. If not controlled, hotspot generation might cause potential catalyst deactivation or risk of reactor explosion. Pilot-scale systems for solid-phase processing such as pyrolysis have already been demonstrated, whereas large-scale microwave-assisted liquid-phase processing could face problems such as low microwave absorptivity in hot water and limited microwave penetration for large volumes. Further work is needed to develop standard protocols to clarify the advantages of microwaves in wide-ranging biorefinery systems to lay the foundation of technological transfer.</p>