According to the present invention, there is provided a cleaning system for biomass material handling systems and methods for such system. The cleaning system for a biomass material treatment stage in a continuous process system includes a hydrolysis or pre-hydrolysis reactor, a feeding arrangement is arranged to continuously feed biomass material to an inlet of the reactor, wherein reactor includes a reactor screw for moving the biomass material through the reactor and a discharge pipe including a discharge screw for continuously discharging treated biomass material. At least one high-pressure cleaning nozzle is arranged inside a housing of said reactor, wherein the at least one high-pressure cleaning nozzle is arranged to eject cleaning agent at predetermined intervals during operation of the reactor.