The behavior and mechanism of thallium (Tl) adsorption by biogenic manganese oxides (BMnOx) are poorly understood. In this study, BMnOx was applied for Tl(I) removal from aqueous solution, and the adsorption interactions were systematically revealed for the first time. BMnOx was successfully prepared with high productivity by effectively oxidizing Mn(II) with a manganese oxide bacterium in an optimal Mn(II) concentration range of 4.0–28 mg/L. Compared with other adsorbents, the prepared BMnOx achieved high Tl(I) adsorption capacity over a wide pH range from 3.0 to 9.0 and high humic acid (HA) concentration (40 mg/L) interference. The experimental results were well depicted by pseudo-second-order kinetics and the Langmuir isotherm model, indicating that chemisorption played the dominant role during the adsorption process. The adsorption mechanisms were verified as synergetic interactions of oxidation-precipitation, electrostatic attraction, ion exchange and surface complexation. X-ray photoelectron spectroscopy (XPS) and transmission electron microscopy (TEM) results suggested that 19.46% of the highly toxic Tl(I) was transformed into the much less toxic product Tl₂O₃ after adsorption onto BMnOx. This study provides theoretical guidance for high-concentration Tl(I) decontamination from groundwater by biogenic manganese oxides.