•Behavior of natural radionuclides (238U, 232Th and their decay products, 40K) in the Bayer process was analyzed.•Thorium and its decay product 228Ra were found only in bauxites and bauxite residue.•Minor portion of uranium was found to dissolve in the process liquors and 3% of the input content ended up in alumina.•40K dissolved and moderately accumulated in the process liquors, however it did not end up in the alumina.•From the radiation protection perspective, all the materials analyzed in the current study pose no radiological hazard. Naturally occurring radionuclides were studied through the Bayer process by calculating their mass flows. Aluminium of Greece (AoG) provided sample materials and plant data from several process stages. Measurements of radionuclide concentrations were carried out by gamma-ray spectroscopy. The performed measurements show that in the specific case of the AoG plant, the majority of the natural radionuclides were introduced with karst bauxites, which showed higher activity concentrations for nuclides compared to lateritic bauxites. Most of these nuclides accumulated in the bauxite residue, while only a minor portion of uranium isotope 238U was found in alumina, corresponding to 3% of its input value. Uranium was observed to partially dissolve in the process liquors similarly to 40K, whereas the latter was not associated with aluminium hydroxide. All the materials studied in the current research work had radionuclide concentrations well below the exemption limits set by EURATOM Basic Safety Standard, indicating that these naturally occurring radionuclides do not pose a radiological hazard for workers of the AoG plant or the public.