One of the challenges in Fischer–Tropsch synthesis (FTS) is the high reduction temperatures, which cause sintering and the formation of silicates. These lead to pore blockages and the coverage of active metals, particularly in conventional catalyst promotion. To address the challenge, this article investigates the effects of the preparation method, specifically the inverse promotion of SiO2-supported Co catalysts with manganese (Mn), and their reduction in H2 for FTS. The catalysts were prepared using stepwise incipient wetness impregnation of a cobalt nitrate precursor into a promoted silica support. The properties of the catalysts were characterized using XRD, XPS, TPR, and BET techniques. The structure–performance relationship of the inversely promoted catalysts in FTS was studied using a fixed-bed reactor to obtain the best performing catalysts for heavy hydrocarbons (C5+). XRD and XPS results indicated that Co3O4 is the dominant cobalt phase in oxidized catalysts. It was found that with increase in Mn loading, the reduction temperature increased in the following sequence 10%Co/SiO2 < 10%Co/0.25%Mn-SiO2 < 10%Co/0.5%Mn-SiO2 < 10%Co/3.0%Mn-SiO2. The catalyst with the lowest Mn loading, 10%Co/0.25%Mn-SiO2, exhibited higher C5+ selectivity, which can be attributed to less MSI and higher reducibility. This catalyst showed the lowest CH4 selectivity possibly due to lower H2 uptake and higher CO chemisorption.