A fuel supply system has a fuel tank, a first fuel pump, and a first oxygen removal unit. The first fuel pump delivers fuel from the fuel tank into the first oxygen removal unit. A valve downstream of the first oxygen removal unit is operable to selectively deliver fuel back to the fuel tank in a bypass position or downstream to a use in a use position. A controller programmed to control the valve and the first fuel pump maintains the valve in the bypass position when an associated gas turbine engine is not operating. The controller moves the valve to the use position when the associated gas turbine engine is operating. A gas turbine engine and a method of operating a fuel supply system are also disclosed.