Effective neutralization of strongly alkaline conditions in bauxite residues (BR) is the fundamental step to initiate the process of eco-engineering BR into growth substrate (or soil-like medium) for direct phytostabilization with pioneer plant species. The present study aimed to evaluate the effectiveness of microbial decomposition of organic matter (OM) (i.e., biomass residues) in neutralizing the strong alkalinity of residues under saturated conditions, together with the regulatory role of calcium sulfate (CaSO4) addition. Admixing OM (i.e., sugarcane mulch, Lucerne hay) alone in the BR significantly lowered the porewater pH from 11.4 to around 9.0 by Day 7, which persisted until the end of incubation (Day 28). The pH reduction in the porewater of OM-amended BR coincided with the production of acidic organic compounds (mainly acetic acid). Diverse species of organotrophic bacteria (e.g., Enterobacteriales, Pasteurellales, Lactobacillales, and Streptophyta) were found to have colonized in the OM-amended BR, but which were dominated by haloalkaliphilic bacteria (e.g., Halomonas and Bacillaceae). The CaSO4 addition in the OM-amended BR further lowered pH to 8.3 in the porewater. Besides, the bioneutralization effects resulted in dramatic reduction (>90%) of soluble Al in the porewater, which is a prerequisite to lowering Al toxicity in plants. At the same time, the levels of major cations (i.e., K, Ca, Mg) in the porewater were elevated by the OM + CaSO4 amendment, which would facilitate subsequent leaching of these soluble salts to lower the salinity in the BR, and improve the diversity of organotrophic bacterial communities in the amended BR.