During required change-over to a holding operation in a Fischer-Tropsch synthesis, the reactor is not depressurized after cutting off the supply of fresh synthesis gas to the Fischer-Tropsch reactor, and the temperature is not reduced to below the temperature below which a Fischer-Tropsch reaction no longer takes place. Instead, the reactor is charged with an inert gas, e.g., kept in a vessel at a pressure higher than the operating pressure of the Fischer-Tropsch synthesis, until the reacting components have been flushed out from the Fischer-Tropsch system. While maintaining the pressure and the temperature, the reactor is thus merely inerted for a few seconds, sufficient to interrupt the Fischer-Tropsch reaction. Catalyst damage is avoided, and the liquid phase situation on the catalyst is at least essentially unchanged, facilitating subsequent re-commissioning of the catalyst.