Every year, thousands of patients die from nosocomial infections got in hospital after surgical intervention. Those infections are directly linked to bacterial contamination of medical devices surfaces that are used during operation. Moreover, interaction of specific biomolecules like phospholipids or lipopolysaccharides (LPS) or certain proteins with organisms can be a major cause of diseases. Prominent examples are pyrogenes - lipopolysacharides (LPS) and lipoteichoic acids (LTA) -, which cause fever in human body and are potentially lethal after contact with blood. In some cases the secondary or tertiary structure of proteins is responsible for their biological properties. Important example is PrP (prion) which becomes pathogenic after a change of its structure. The contaminated surface (e.g. medical devices, accessories, work surface or tissue) cannot be decontaminated with current sterilisation practices without inducing major damage to the substrate or tissue itself, because of the high temperature used, or chemical reaction with the surface. In the present work, the inactivation or modification of biologically potentially harmful molecules is addressed in a combined approach using low pressure plasma discharges with non toxic gas mixtures. The emerging species fluxes of these plasmas are measured. Different characteristic biomolecules (LPS, LTA, proteins etc. as well as whole micro-organism cells) are exposed to the plasmas and the changes induced are monitored in-situ using infrared spectroscopy as well as ex-situ using biochemical and structural analysis as a function of the gas mixture and plasma parameters. Different potential mechanisms (etching, UV radiation, chemical reactions) are presented. The gained knowledge on the interaction of plasma discharges with pathogenic biomolecules and microorganisms allows a targeted development of decontamination strategies for very resistant species. The potential applications are in the field of surface decontamination and sterilisation of medical objects and opens large possibilities of applications in the field of security.