Organic matter, serving as a carbon source and energy provider for microbial activities driving manganese oxidation in soil, plays a vital role in the biogeochemical processes underlying the formation of biological manganese oxides (BMOs) and regulating heavy metal (HMs) mobility within soil profiles. The interactions between BMOs and organic matter, their environmental behavior, and practical field applications remain poorly understood. In this study, the remediation effectiveness of organic fertilizer (OF) and manganese-oxidizing bacteria (B) in addressing arsenic (As), cadmium (Cd), and lead (Pb) co-contamination in soil was evaluated, alongside the resulting elemental migration within the soil profile, uptake by maize, and post-remediation soil health. A 400-day field experiment demonstrated that compared with the control, treatment with 1.0 % organic fertilizer promoted the transformation of HMs chemical form from relatively active to stable fraction, significantly controlling Cd and Pb accumulation in maize roots (p < 0.05). Conversely, treatment of B decreased the bioavailability of As by 23.9 % but increased the bioavailability of Cd and Pb by 10.9 % and 20.2 %, respectively. Thus, it significantly increased Pb content in leaves and additional attention should be paid to its feed and food health risks. Under the combined BOF treatment (bacteria + organic fertilizer), high fixation efficiency of As (42.3 %), Cd (16.8 %), and Pb (13.2 %) was achieved through chemical transformation, reduced leaching risks, break the nucleation spatial locations, and the microbial-mineral pump mechanism. BOF treatment also significantly increased the relative abundance of Actinomycetes (+15.8 %) and Proteobacteria (+13.3 %) at the phylum level, suggesting those microorganisms possibly were persistently recruited in biomineralization nucleation. Soil enzyme activity analysis revealed that only treatment B reduced sucrase activity, while urease and catalase activities were not significantly affected in any treatment. Principal component analysis indicated that pH was a critical environmental driver of the biogeochemical cycling of Cd and Pb. Furthermore, maize absorption of nutrients such as iron and phosphorus influenced the transport and mobility of HMs. This study highlights the effectiveness of BOF treatment in simultaneously stabilizing As, Cd, and Pb, while enhancing the adaptability of in-situ remediation materials to the soil, making it a promising strategy for remediating HMs-contaminated soils.