Management of Be contamination using industrial solid waste or solid waste-derived amendments is not well understood. This study investigated the potential of Australian coal fly ash (CFA), derived synthesized zeolite (SynZ) and chitosan-modified zeolite (ModZ), for Be immobilization at the Little Forest Legacy Waste Site (LFLS), a low-level radioactive waste disposal site near Sydney, Australia. In laboratory simulation experiments, the SynZ and ModZ were separately applied as an amendment to both naturally contaminated soil and simulated contaminated (spiked) soil. Different techniques, including pore water (PW), batch desorption, and microbial activities were assessed to provide insight into immobilization mechanisms. Results revealed that amendment of 2% ModZ in soils, substantially decreased Be concentrations in PW (PWBe) ranging from 13.3% to 99.5% across all concentrations of Be. In contrast, PWBe increased while using SynZ, which could be attributed to the increased solubility of different organic-inorganic elements in PW. Moreover, batch desorption using Milli-Q water, simulated acid rainwater [H2SO4/HNO3 = 60/40, (v/v), and 0.11 M acetic acid solution also revealed similar patterns of Be immobilization as found in PWBe analysis. Soil amendments boosted microbial biomass carbon, and phosphorous (MBC,P), along with basal respiration (BRCO2). This indicates increased microbial activities, which are linked with environmental eco-friendliness. This effect was substantially noticed in ModZ-amended soils, exhibiting up to 22 times higher in BRCO2 values compared to unamended soil. Additionally, reduced PWBe was correlated with soluble organic-inorganic elements, desorbed Be in the batch study, and soil MBc. The differences in behavior between SynZ and ModZ underline the importance of carefully studying the various potential amendment materials and the need to evaluate their performance before application in field situations. This study highlights ModZ's effectiveness in eco-friendly Be immobilization, underlining the role of organic functional groups in zeolite architecture, a key factor in controlling Be in soils.