Electron energy loss spectroscopy (EELS), X-ray photoelectron spectroscopy (XPS), and transmission electron microscopy have been used to study iron catalysts for Fischer–Tropsch synthesis. When silica-containing iron oxide precursors are activated in flowing CO, the iron phase segregates into iron carbide crystallites, leaving behind some unreduced iron oxide in an amorphous state coexisting with the silica binder. The iron carbide crystallites are found covered by characteristic amorphous carbonaceous surface layers. These amorphous species are difficult to analyze by traditional catalyst characterization techniques, which lack spatial resolution. Even a surface-sensitive technique such as XPS shows only broad carbon or iron peaks in these catalysts. As we show in this work, EELS allows us to distinguish three different carbonaceous species: reactive amorphous carbon, graphitic carbon, and carbidic carbon in the bulk of the iron carbide particles. The carbidic carbon K edge shows an intense “π*” peak with an edge shift of about 1 eV to higher energy loss compared to that of the π* of amorphous carbon film or graphitic carbon. EELS analysis of the oxygen K edge allows us to distinguish the amorphous unreduced iron phase from the silica binder, indicating these are two separate phases. These results shed light onto the complex phase transformations that accompany the activation of iron catalysts for Fischer–Tropsch synthesis.