We investigated the effect of pre-treatment conditions on the activity and selectivity of cobalt catalysts for Fischer–Tropsch synthesis (FTS) by varying both the reduction atmosphere and the reduction temperature. Catalysts supported on SiO2, Al2O3, and TiO2, prepared via incipient wetness impregnation, were evaluated, and activation temperatures in the range 250–350 °C were considered. Activation with syngas led to a better product selectivity (low CH4, high selectivity to liquid hydrocarbons, and low paraffin to olefin ratio (P/O)) than the catalysts reduced in H2 at lower activation temperatures. The CoxC species suppressed the hydrogenation reaction, and it is hypothesised that this resulted in the high selectivity of olefins observed for the syngas pre-treated catalysts. On the basis of the experimental results, we postulated that a synergistic effect between Co0 and CoxC promotes the production of the long chain hydrocarbons and suppresses the formation of CH4. In addition, for systems aimed at producing lower olefins, syngas activation is recommended, and for the FTS plants that focus on maximising the production of higher molecular weight products, H2 activation might be considered. These results provide insights for the future FTS catalyst design and for target product-driven operations.