Thin films of human serum albumin (HSA) were immobilized on polystyrene (PS) substrates previously functionalized either with polar or nonpolar functional groups. The functionalization was performed by treatment with cold gaseous plasma created in pure oxygen and tetrafluoromethane (CF4) plasmas, respectively. Samples were examined with soft X-rays in the photon energy range of 520 to 710 eV in the ANTARES beam line at SOLEIL Synchrotron. NEXAFS spectra of O K-edge and F K-edge were collected at different spots of the sample, and measurements at each spot were repeated many times. A strong degradation of the HSA protein was observed. The weakly irradiated samples exhibited strong absorption at 531.5 eV associated with the O 1s→π*amide transitions, and a broad non distinctive peak at 540 eV was attributed to the O 1s→σ*C–O transitions. Both peaks decreased with increasing irradiation time until they were completely replaced by a broad non-distinctive peak at around 532 eV, indicating the destruction of the original protein conformation. The shortage of the amide groups indicated breakage of the peptide bonds.