Developments in chemistry, materials science and biology have been fuelled by our search for structure–property relationships in matter at different levels of organization. Transformations in chemical synthesis and living systems predominantly take place in solution, such that many efforts have focused on studying nanoscale systems in the liquid phase. These studies have largely relied on spectroscopic data, the assignment of which can often be ambiguous. By contrast, electron microscopy can be used to directly visualize chemical systems and processes with up to atomic resolution. Electron microscopy is most amenable to studying solid samples and, until recently, to study a liquid phase, one had to remove solvent and lose important structural information. Over the past decade, however, liquid-phase electron microscopy has revolutionized direct mechanistic studies of reactions in liquid media. Scanning electron microscopy and (scanning) transmission electron microscopy of liquid samples have enabled breakthroughs in nanoparticle chemistry, soft-matter science, catalysis, electrochemistry, battery research and biochemistry. In this Review, we discuss the utility of liquid-phase electron microscopy for studying chemical reaction mechanisms in liquid systems.