This paper presents the results of computer simulation in COMSOL Multiphysics of the hydrogen isotopes beam dynamics extracted from a plasma source of small linear accelerator. The beam energy was 100 keV. The simulation was carried out taking into account the charge exchange of ions on neutral gas molecules in the accelerating system. At the same time, the calculations took into account the process of secondary ion-electron emission from the surfaces of the accelerating system that are bombarded with both fast and slow ions. Consideration of this process made it possible to determine that the value of the electronic load is at least 50% of the main beam current of 100 μA. The inclusion in the trajectory analysis the magnetic field simulation in the secondary electrons generation area made it possible to determine the magnetic field strength, which effectively blocks secondary electrons on the target (3000 Gauss). Then it has been experimentally demonstrated that the discharge current in a plasma source automatically increases by 20% when using the magnetic suppression system on the target node (magnetic field strength is 3000 Gauss).