The modern chemical industry uses heterogeneous catalysts in almost every production process. They commonly consist of nanometre-size active components (typically metals or metal oxides) dispersed on a high-surface-area solid support, with performance depending on the catalysts' nanometre-size features and on interactions involving the active components, the support and the reactant and product molecules. To gain insight into the mechanisms of heterogeneous catalysts, which could guide the design of improved or novel catalysts, it is thus necessary to have a detailed characterization of the physicochemical composition of heterogeneous catalysts in their working state at the nanometre scale. Scanning probe microscopy methods have been used to study inorganic catalyst phases at subnanometre resolution, but detailed chemical information of the materials in their working state is often difficult to obtain. By contrast, optical microspectroscopic approaches offer much flexibility for in situ chemical characterization; however, this comes at the expense of limited spatial resolution. A recent development promising high spatial resolution and chemical characterization capabilities is scanning transmission X-ray microscopy, which has been used in a proof-of-principle study to characterize a solid catalyst. Here we show that when adapting a nanoreactor specially designed for high-resolution electron microscopy, scanning transmission X-ray microscopy can be used at atmospheric pressure and up to 350 degrees C to monitor in situ phase changes in a complex iron-based Fisher-Tropsch catalyst and the nature and location of carbon species produced. We expect that our system, which is capable of operating up to 500 degrees C, will open new opportunities for nanometre-resolution imaging of a range of important chemical processes taking place on solids in gaseous or liquid environments.