For safety assessment purposes, it is necessary to study the mobility of long-lived radionuclides in the geosphere and the biosphere. Within this framework, we studied the behaviour of 99Tc in biologically active organic matter-rich soils. To simulate the redox conditions in soils, we stimulated the growth of aerobic and facultative denitrifying and anaerobic sulphate-reducing bacteria (SRB). In the presence of either a pure culture of denitrifiers (Pseudomonas aeruginosa) or a consortium of soil denitrifiers, the solubility of TcO4− was not affected. The nonsorption of TcO4− onto bacteria was confirmed in biosorption experiments with washed cells of P. aeruginosa regardless of the pH. At the end of denitrification with indigenous denitrifiers in soil/water batch experiments, the redox potential (EH) dropped and this was accompanied by an increase of Fe concentration in solution as a result of reduction of less soluble Fe(III) to Fe(II) from the soil particles. It is suggested that this is due to the growth of a consortium of anaerobic bacteria (e.g., Fe-reducing bacteria). The drop in EH was accompanied by a strong decrease in Tc concentration as a result of Tc(VII) reduction to Tc(IV). Thermodynamic calculations suggested the precipitation of TcO2. The stimulation of the growth of indigenous sulphate-reducing bacteria in soil/water systems led to even lower EH with final Tc concentration of 10-8 M. Experiments with glass columns filled with soil reproduced the results obtained with batch cultures. Sequential chemical extraction of precipitated Tc in soils showed that this radionuclide is strongly immobilised within soil particles under anaerobic conditions. More than 90% of Tc is released together with organic matter (60–66%) and Fe-oxyhydroxides (23–31%). The present work shows that ubiquitous indigenous anaerobic bacteria in soils play a major role in Tc immobilisation. In addition, organic matter plays a key role in the stability of the reduced Tc.