Cadmium (Cd) pollution poses a serious threat to aquatic environmental safety and sustainable agricultural development. Biogenic iron (Fe)-manganese (Mn) oxides (BFMO), mediated by Mn-oxidizing bacteria, are promising natural adsorbents for Cd removal. Although iron-manganese oxides have been widely studied for application in wastewater treatment, BFMO synthesized via a fully biologically driven process using novel strains still face limitations in terms of material structure and the availability of active sites. In this study, BFMO was synthesized using a newly isolated strain of Stenotrophomonas sp. Z-MRQA-3, and its mineralogical properties, Cd(II) immobilization performance, and underlying mechanisms were systematically investigated. The results demonstrated that BFMO possesses a high specific surface area (244.52 m2/g), a hierarchical porous structure, and abundant surface functional groups, which collectively contribute to its superior adsorption capacity. Under conditions of adsorbent dosage of 0.5 g/L, initial Cd(II) concentration of 50 mg/L, and pH 7.2, the removal efficiency of Cd(II) reached 96.52%, with an adsorption capacity of 80.83 mg/g. The adsorption process followed the pseudo-second-order kinetic model and the Langmuir isotherm model, with a theoretical maximum adsorption capacity of 89.29 mg/g. Mechanistic studies indicated that Cd(II) immobilization occurs mainly through surface complexation, ion exchange, and co-precipitation, facilitated by the redox-active multivalent Mn and oxygen-containing functional groups. This study aims to investigate the unique advantages of in situ synthesizing BFMO using specific bacterial strains. This work offers fundamental insights and practical prospects for developing green, efficient, and sustainable technologies for remediating Cd-contaminated water.