Radioactive technetium-99 (99Tc) is present in nuclear and medical waste. Its immobilization by magnetite (FeIIFeIII2O4) has been studied in the last decades, showing that magnetite reduces pertechnetate (TcVIIO4−) to TcIV, which is either incorporated into the magnetite structure or forms TcIV-TcIV-dimers. The distribution between both phases as well as the incorporation mechanism remain, unclear. This work investigates the molecular environment of Tc after putting it in contact with presynthesized nanoparticulate magnetite as a function of pH (2 - 13) and time (up to 7 weeks). X-ray absorption spectroscopy (XAS) was combined with density functional theory methods (DFT) to decipher the mechanism of TcIV incorporation. We observed that sorption of TcIV-TcIV-dimers initially occurs at pH 5 and pH 7, while TcIV incorporation in magnetite prevails at longer times and at pH 10. We suggest that TcIV-TcIV-dimer sorption on magnetite is due to maghemitization, whereas TcIV incorporation is due to the electron transfer from sorbed Fe2+ through magnetite and subsequent release of FeII in solution (redox conveyor belt model), “burying” TcIV into the magnetite structure. DFT calculations indicate that TcIV incorporates in magnetite by an exchange of two FeII atoms for one TcIV, keeping the charge balanced by creating a vacancy.