Electrons with energies of 300 keV or lower have the potential to decontaminate the surfaces of various types of food products with minimal loss of quality. The aim of the present work was to determine the thickness of the layer inhabited by microorganisms. The food samples tested were black and white pepper irradiated with 200 keV, 230 keV, 300 keV and 9 MeV beams of electron energy. To determine the depth from the surface which can be inhabited by microorganisms two approaches were tested. The methods used were based on the application of different microbiological recovery techniques and the microbial effectiveness of the irradiation process depending on the energy of the electron beam. It was observed that the layer which microorganisms may contaminate differed for the tested samples it was estimated as being below 100 μm thick for white pepper and about 200 μm for black pepper. The penetration ability was significant in experiments performed, and as a result the electron beam at the lowest levels tested (200 and 230 keV) was found to be insufficient to effectively decontaminate the black pepper samples. The beam of energy 300 keV was found to have a similar microbial inactivation effect as the high energy electron beam (9 MeV).