Abstract Plasma treatment and plasma polymerization processes aiming to form amine groups on polystyrene surfaces were studied in-silico with molecular dynamics simulations. The simulations were compared with two experiments, (i) plasma treatment in N₂/H₂ bipolar pulsed discharge and (ii) plasma polymerization in cyclopropylamine/Ar radio frequency (RF) capacitively coupled discharge. To model favorable conditions for the incorporation of primary amine groups, we assumed the plasma treatment as the flux of NH₂ radicals and energetic NH₃ ions, and the plasma polymerization as the flux of cyclopropylamine molecules and energetic argon ions. It is shown in both the simulation and the experiment that the polystyrene treatment by the bipolar pulsed N₂/H₂ plasmas with an applied voltage of about ±1 kV formed a nitrogen-rich layer of a thickness of only a few nm. The simulations also showed that, as the NH₃ incident energy increases, the ratio of primary amines to the total number of N atoms on the surface decreases. It is because the energetic ion bombardment brakes up N–H bonds of primary amines, which are mostly brought to the surface by NH₂ radical adsorption. Our previous experimental work on the CPA plasma polymerization showed that increased RF power invested in the plasma leads to the deposition of films with lower nitrogen content. The MD simulations showed an increase of the nitrogen content with the Ar energy and a limited impact of the energetic bombardment on the retention of primary amines. Thus, the results highlighted the importance of the gas-phase processes on the nitrogen incorporation and primary amines retention in the plasma polymers. However, the higher energy flux towards the growing film clearly decreases amount of hydrogen and increases the polymer cross-linking.