Candida spp are present in 70%-90% of invasive infections and non-thermal plasmas operated at atmospheric pressure have been gaining attention as a new antimicrobial strategy for medical devices. This work presents studies on the inactivation efficacy of biofilms of Candida albicans grown in polyurethane (PU), main constituent of central venous catheter, by atmospheric gliding arc plasma jet operated at different process parameters: gas chemistry/flow(argon, helium, or its mixture with air) and plasma pulsing. The investigation was performed in the post-discharge region of the plasma jet. After plasma treatment, the colony-forming units(CFU)were counted, and the chemical bonding (FT-IR) and morphological (SEM) analyses of the surface of the biofilm plus PU substrate were investigated. Furthermore, optical emission spectroscopy (OES) technique was applied to characterize the plasma chemistry and measure the OH concentration and rotational temperature, together with thermal analyses of the substrate during treatment. CFU results showed that gliding arc plasma jet was efficient for the inactivation of C. albicans biofilms. It obtained a maximum CFU reduction of 100% and 98% for 4 L min-1 air/6 L min-1 He and 99% and 98% for 4 L min-1 air/6 L min-1 Ar in continuous and pulsed mode, respectively. SEM and FT-IR analyses corroborate with results of % CFU reduction, showing a reduction of the biofilm constituents on the substrate surface. From OES and substrate thermal analyses, it was possible to verify that, although the OH concentration and rotational temperature of air/He plasma jet are lower in comparison to the air/Ar, a drastic increase of the substrate temperature during the treatment (up to 70 °C)was observed for this plasma chemistry.