Abstract: Technetium-99(⁹⁹Tc) is a long-lived fission product in the nuclear fuel cycle. Predominantly existing as the highly soluble and mobile pertechnetate anion(\mathrmTcO_4^-, Tc(Ⅶ)), it poses significant challenges for immobilization in natural environments and is considered a key radionuclide in the long-term safety assessment of high-level radioactive waste repositories. Microbial processes can reduce Tc(Ⅶ) to insoluble Tc(Ⅳ) precipitates, altering its environmental mobility. In this study, two indigenous microbial strains—Klebsiella variicola X-21(Gram-negative) and Bacillus cereus X-68(Gram-positive)—were systematically investigated for their capacity to reduce and immobilize Tc(Ⅶ) in three representative natural media: soil, Tamusu clay, and Beishan granite. Batch experiments revealed that abiotic media exhibited negligible sorption capacity, while microbial activity significantly enhanced Tc(Ⅶ) reduction, with efficiency positively correlated with inoculum concentration. However, \mathrmNO_3^- strongly inhibited Tc reduction in the soil system. Dynamic column tests show that microbial processes effectively delay Tc breakthrough and effluent release, with pre-reduced Tc products exhibiting high retention(up to 98%) over 450 h of continuous leaching. Under oxic conditions, partial reoxidation and remobilization are observed; nevertheless, Tc(Ⅳ) products generate by Klebsiella variicola X-21 displayed greater redox stability than those formed by Bacillus cereus X-68. Overall, the findings highlight that Tc immobilization in complex natural matrices is governed by microbially mediated reduction processes, strongly influenced by the composition of the matrix and prevailing redox conditions. This study provides new experimental insights into the biogeochemical mechanisms controlling Tc behavior in natural environments and offers a scientific basis for in situ bioremediation strategies, engineered barrier design, and safety assessment of geological repositories in China.