Rapid industrialization and urbanization have resulted in the widespread contamination of soil by potentially toxic metal(loid)s (PTMs). Among these, arsenic (As), cadmium (Cd), chromium (Cr) lead (Pb) and nickel (Ni) are particularly concerning, affecting millions of hectares of arable land globally and posing significant threats to food security and human health. Biochar (BC) has emerged as a promising soil amendment due to its ability to mitigate soil pollution by immobilizing contaminants. But how biochar-linked free radicals affect this process in plants and soil remains murky. Additionally, the mechanism of the geochemical transformation of PTMs in soil-plant systems influenced by biochar-based free radicals is unclear. Here, the influence of free radicals on immobilization, and transformation of PTMs in the soil-plant system under various BC and Comp treatment was investigated. Six treatment groups (1% and 2% biochar, compost, combined application, and control) were randomly assigned to pots in a randomized complete block design (RCBD) to test their effects on maize growth. Results revealed that there was a noticeable rise in the concentration of free radicals in both the BC and Comp treatments compared to the control and the combined application of BC and Comp treatments. The biochar treatment showed a slight reduction in these functional groups, suggesting possible adsorption or sequestration onto the BC surface while the Comp treatment led to an increase in functional groups associated with carbohydrates, proteins, and lipids, indicating enhanced organic matter content. The combined treatment exhibited intermediate effects, suggesting a synergistic interaction between Comp and biochar. X-ray diffraction analysis indicated that the BC did not demonstrate significant alterations in soil mineralogy, suggesting minimal direct effects on mineral dissolution or transformation. Conclusively, biochar-generated free radicals, especially hydroxyl radicals (•OH), play a crucial role in PTMs (i.e., Cd, Cr, Ni, As and Pb) immobilization in soil-plant systems. This study provides novel insights into biochar's mechanisms for mitigating PTMs pollution, paving the way for optimized soil amendment strategies.