A system combining XRD and DRIFTS characterization techniques was developed to monitor the structure and the surface of a cobalt catalyst during the Fischer–Tropsch synthesis. In the present study, several phenomena could be observed and discriminated. Firstly, residual cobalt oxide was found to further reduce during the reaction, but this enhancement in reduction degree did not clearly lead to a gain of activity. Secondly, the formation of linear and bridged carbonyls took place rapidly at the surface of the catalyst. A surprising increase in activity was observed while the concentration of carbonyls decreased, supporting the idea that CO dissociation was a crucial step in the Fischer–Tropsch mechanism. Arising from that, the increase in activity was attributed to surface reconstruction which transforms sites favoring strong CO adsorption into sites active for CO dissociation. Finally, most of the catalyst deactivation was assigned to the formation of surface oxygenate species, which were suspected to result from the reduction of CoO with hydrocarbons.