This paper focuses on the use of in situ and ex situ characterisation techniques to provide evidences of carbon species on a commercial iron-based Fischer-Tropsch synthesis catalyst as well as other indices of potential deactivation mechanisms. In situ XANES measurements demonstrate that re-oxidation or transformation of the active iron phase, i.e. the Hagg carbide phase, was not a significant deactivation mechanism at the studied conditions. Sintering of Hagg carbide nanoparticles is significant with increasing temperatures and time on stream. The sintering mechanism is proposed to be a hydrothermally-assisted process. In situ DRIFTS indicates the presence of different carbon species on the catalyst surface such as aliphatic hydrocarbons from wax products and oxygenate compounds such as alcohols, aldehydes/ketones and carboxylate species. Carboxylate species are resistant towards hydrogenation at 280 degrees C. The presence of different carbon species on the surface after wax product extraction is evident from TPH-MS measurements. GC-MS analysis shows that the strongly adsorbed carbon species remaining on the catalyst surface from wax products are mainly alpha-olefins and branched carboxylic species. The interaction of oxygenate compounds, especially carboxylate species with iron oxide, may form stable complexes limiting further iron catalyst carburization. STEM-EDX analysis shows that carbon is preferentially located on iron particles.