A method for filling a container (2) with a filling product, comprising the steps of: positioning the container (2) in a filling station (1) so that its mouth (2b) is below the filling valve (9); separating a treatment volume (40) of the neck (2a) comprised between the filling valve (9) and at least one part of the neck (2a) of the container (2) from an external environment (6) containing the body (2d) of the container (2); dispensing plasma into the treatment volume (40) so that it flows over the neck (2a) of the container (2); enabling the filling valve (9) to dispense the filling product into the container (2).