The method consists of filling a soft container (2) comprising two thin sheets sealedly joined together along a bounding perimeter by the following steps: providing an internally sterile container (2), inserting a nozzle (8) with a delivery mouth (9) through an aperture (5) formed in the container (2), conveying the fluid material into the container through said mouth (9), extracting the nozzle (8) from the container (2) after conveying the material; closing said aperture (5) by sealing the two sheets of the container (2). The filling machine comprises: a sealing box (3) comprising two complementary half-boxes (4a, 4b); clamping means for clamping together and unclamping said two half-boxes (4a, 4b) along respective sealing edges (21, 22, 23), to isolate its interior from the outside environment; aperture-forming means (26a, 26b, 26c) located in said sealing box (3) to form an aperture (5) in that portion of the container (2) inserted in the box (3); filling means (8, 9) for filling the container (2) through the aperture (5); welding means (32) for sealing said aperture (5) on termination of filling.