The invention concerns a method for treating a surface for the protection and functionalisation of polymers (4) by gas plasma deposit in a confined chamber (10) of one or several silicon alloy layers (43). The silicon alloy is selected among silicon and its oxides, nitrides, oxynitrides; the deposit is performed at a temperature less than the degradation temperature of the polymer, and a physico—chemical surface pre-treatment by plasma is performed in the same chamber before the silicon alloy is deposited; the pre-treatment consisting in a surface treatment comprising etching a surface zone of the polymer and step which consists in depositing a polymeric carbon compound.