The influence of organic capping agents on the performance of Ru nanoparticles in aqueous-phase Fischer–Tropsch (FT) synthesis was investigated. Three organic capping agents were used: trimethyl(tetradecyl)ammonium bromide (TTAB), polyvinylpyrrolidone (PVP), and sodium 3-mercapto-1-propanesulfonate (SMPS). To exclude the effects of particle size, the capping agents were placed onto carbon-nanofiber-supported Ru nanoparticles of size 3.4 nm. The activity in the FT reaction increased in the order: Ru-SMPS≪Ru-PVP<Ru-TTAB<Ru. Kinetic data suggest that the FT mechanism was largely unaffected by the presence of capping agents; thus, their binding to active centers explains activity trends. Replacing water with n-hexadecane as the solvent results in an increase in the rate of formation and a decrease in the chain-growth probability for hydrocarbons, whereas the production of oxygenates is unaffected. This trend is consistent with the proposal that hydrocarbons are formed on reaction centers that involve facile CO dissociation and that termination is the rate-determining step. For oxygenates, CO dissociation is proposed to be the rate-determining step.