The effects of modification with zirconia on the properties of cobalt species in cobalt Fischer–Tropsch catalysts supported by mesoporous silicas with different porous structures were investigated using nitrogen adsorption, X-ray diffraction, temperature programmed reduction, in situ magnetic measurements and X-ray absorption. The catalysts were prepared by sequential incipient impregnation using solutions of cobalt nitrate and zirconyl nitrate. The effects of zirconia modification on the structure and performance of cobalt based catalysts differ considerably with cobalt catalysts supported by smaller pore MCM-41 and larger pore SBA-15 silicas. In SBA-15 supported samples, modification with zirconia did not result in any significant change in cobalt reducibility and dispersion. Therefore, the concentration of active cobalt metal surface sites on all SBA-15 supported catalysts was comparable, which led to the similar catalytic performance in Fischer–Tropsch synthesis. In MCM-41 supported cobalt catalysts zirconia promotion weakened the cobalt–silica interaction and led to the preferential localization of Co 3O 4 crystallites on the outer surface of the support. Higher zirconia loading led to larger cobalt particles in the zirconia-modified CoMCM-41 catalysts which displayed easier cobalt reduction. The catalytic activity of CoMCM-41 catalysts in Fischer–Tropsch reaction passed through a maximum as a function of zirconia content. The highest activity corresponded to the maximum concentration of cobalt metal sites.