A combination of time-resolved synchrotron μ-X-ray diffraction computed tomography (μ-XRD-CT) and μ-pair distribution function computed tomography (μ-PDF-CT) has been applied for the study of an individual Co/γ-Al₂O₃ catalyst pellet during reduction and the early stages of the Fischer–Tropsch synthesis (FTS) reaction, revealing insight into the solid-state changes occurring from within such crystalline materials. Both sets of data were of sufficient quality so as to be able to follow the spatial dependency of Co speciation evolution from Co₃O₄ to CoO to face-centered cubic (fcc) Co metal nanoparticles. These data revealed the samples to be highly heterogeneous and contain two types of Co species: small (≤6.5 nm) nanoparticles that interact strongly with the γ-Al₂O₃ support which are difficult to reduce (remaining as CoO) and nanoparticles that agglomerate and have little interaction or else are weakly interacting with the support but readily reduce in H₂. The Co phase evolution under FTS conditions shows a strong dependence on the Co nanoparticle location; the complementarity between the observations made using μ-XRD-CT vs μ-PDF-CT allowed us to conclude that at the sample periphery a significant amount of agglomerated, weakly interacting with the support, small fcc Co metal nanoparticles (≤7.5 nm) oxidize to CoO/Co₃O₄ during FTS, most likely due to the presence of water vapor produced during the reaction. Catalytic tests demonstrated that this oxidation coincided with a decrease in CH₄ selectivity and increased water-gas shift (WGS) activity. This oxidation of fcc Co nanoparticles (i.e., the removal of the contribution to the XRD signal) also explains the observation of sintering previously reported for such catalysts in the early stages of the FTS reaction.