We present herein the application of chemical imaging based on energy-filtered TEM in 2 D and 3 D modes to determine the distribution of phases in Co/TiO2–SiC catalysts used in Fischer–Tropsch synthesis. In combination with more traditional techniques such as high-resolution TEM imaging, it allowed us to precisely characterize the microstructure and the relative distribution of the three compounds, Co, Si, and Ti, before and after the catalytic reaction. We show that the TiO2 doping was almost homogenous within the bimodal porous structure of β-SiC. The characteristics of the cobalt nanoparticles depended on the phase they are in contact with: small nanoparticles are found on TiO2 and larger nanoparticles close to SiC. Enhancement of the catalytic performance and higher stability were observed for the Co/TiO2–SiC catalyst relative to Co/SiC, which was attributed to the better dispersion of cobalt on TiO2-doped SiC support and to the relatively strong Co–TiO2 interaction. From a general point of view, this work illustrates that the advanced TEM-based techniques are unavoidable for the characterization and the optimization of heterogeneous catalysts.