A method for handling containers (I) of collapsible type in a filling machine (20) comprising consecutively arranged stations (S1, S2, S3, S4, S5, S6) comprising a filling station (S3) and a gas filling station (S5), the method comprising intermittently moving the containers (I) to the consecutively arranged stations (S1, S2, S3, S4, S5, S6), supplying, at the filling station (S3), liquid product into the product compartment (5) and supplying, at the gas filling station (S5), gas into the handle compartment (7). The filling station (S3) and the gas filling station (S5) are operated such that liquid product is supplied to the product compartment (5) of one of the containers (I) while gas is supplied to the handle compartment (7) of another of the containers (I). The step of supplying gas at the gas filling station (S5) comprises providing a first gas flow (Qi) at a first pressure (Pi) and delivering said first gas flow (Qi) from the nozzle (30) to the handle compartment (7) via said inlet (11), and subsequently providing a second gas flow (Q2) at a second pressure (P2), lower than said first pressure (P1), and delivering said second gas flow (Q2) from the nozzle (30) to the handle compartment (7) via said inlet (11) for establishing a target pressure (PT) inside said handle compartment (7) corresponding to said second pressure (P2).