X-ray diffraction/scattering computed tomography (XRS-CT) was used to create two-dimensional images, with 20 μm resolution, of passivated Co/TiO2/Mn Fischer-Tropsch catalyst extrudates postreaction after 300 h on stream under industrially relevant conditions. This combination of scattering techniques provided insights into both the spatial variation of the different cobalt phases and the influence that increasing Mn loading has on this. It also demonstrated the presence of a wax coating throughout the extrudate and its capacity to preserve the Co/Mn species in their state in the reactor. Correlating these findings with catalytic performance highlights the crucial phases and active sites within Fischer-Tropsch catalysts required for understanding the tunability of the product distribution between saturated hydrocarbons or oxygenate and olefin products. In particular, a Mn loading of 3 wt % led to an optimum equilibrium between the amount of hexagonal close-packed Co and Co2C phases resulting in maximum oxygenate selectivity. XRS-CT revealed Co2C to be located on the extrudates' periphery, while metallic Co phases were more prevalent toward the center, possibly due to a lower [CO] ratio there. Reduction at 450 °C of a 10 wt % Mn sample resulted in MnTiO3 formation, which inhibited carbide formation and alcohol selectivity. It is suggested that small MnO particles promote Co carburization by decreasing the CO dissociation barrier, and the Co2C phase promotes CO nondissociative adsorption leading to increased oxygenate selectivity. This study highlights the influence of Mn on the catalyst structure and function and the importance of studying catalysts under industrially relevant reaction times.