Cobalt nanoparticles play an important role as catalysts for the Fischer–Tropsch synthesis, which is an attractive route for production of synthetic fuels. It is of particular interest to understand the varying conversion rate during the first hours after introducing synthesis gas (H2 and CO) to the system. To this end, several in situ characterization studies have previously been done on both idealized model systems and commercially relevant catalyst nanoparticles, using bulk techniques, such as X-ray powder diffraction and X-ray absorption spectroscopy. Since catalysis takes place at the surface of the cobalt particles, it is important to develop methods to gain surface-specific structural information under realistic processing conditions. We addressed this challenge using small-angle X-ray scattering (SAXS), a technique exploiting the penetrating nature of X-rays to provide information about particle morphology during in situ experiments. Simultaneous wide-angle X-ray scattering was used for monitoring the reduction from oxide to catalytically active metal cobalt, and anomalous SAXS was used for distinguishing the cobalt particles from the other phases present. After introducing the synthesis gas, we found that the slope of the scattered intensity in the Porod region increased significantly, while the scattering invariant remained essentially constant, indicating a change in the shape or surface structure of the particles. Shape- and surface change models are discussed in light of the experimental results, leading to an improved understanding of catalytic nanoparticles.