Development of new techniques for deposition of biologically active coatings in the form of bio-recognition layers in biosensor construction is a current technological challenge. Biosensors are widely applied in environmental protection in determination of hazardous materials, e.g., catechol, hydrochinon or resorcinol. Application of a soft plasma polymerization (SPP) technique by low-energy-density corona discharge has allowed significant simplification of the deposition process of bio-recognition layers. However, the mechanism of the SPP process is by no means fully understood. This paper presents insights into the mechanism of binding laccase enzyme onto graphene oxide (GO) and multi-walled carbon nanotubes (MWCNT) through analysis carried out by density functional theory (DFT) methods and Fourier transform infrared spectroscopy (FTIR). The objective was to examine the mechanism on the basis of binding energies and electrostatic interactions between laccase and carbon nanomaterials as well as enzyme structure after cold plasma deposition. The lowest binding energies have been calculated for the O-N bond between the arginine amino acid of laccase and the hydroxyl group of GO and the C-O bond between the serine molecule of laccase and the carboxyl groups of GO and MWCNT. FTIR and DFT studies showed that the chemical structures of the laccase enzyme and carbon nanomaterials after corona jet plasma treatment are not substantially changed. Preliminary recognition of the mechanism of biosensing layer deposition by the SPP technique opens the way to application of this innovative technique to the construction of other biosensors such as for determination of pollutants in water samples.