Soil, a vital component in biosphere, is frequently endangered to superfluity pollutants, particularly heavy metals. Unlike organic pollutants, heavy metals are persistent and cause environmental, health and socio-economic adverse impacts, Consequently, heavy metals removal from soil ecosystem is not only mandatory but also a topic of interest nowadays. This study assessed four biochemical treatments from a kinetic perspective to evaluate their efficacy in reducing heavy metals concentrations and risks in soils cultivated with tomatoes. The processing materials included: (T1) bentonite + rock phosphate+ phosphate dissolving bacteria (Bacillus megatherium), (T2) bentonite + elemental sulfur + Acidithiobacillus sp., (T3) bentonite + elemental sulfur + rock phosphate + Acidithiobacillus sp. + Bacillus megatherium, and (T4) bentonite + kaolinite clay minerals + rock phosphate+ Bacillus megatherium + elemental sulfur + Acidithiobacillus. Furthermore, two untreated controls were represented by cultivated control and uncultivated control soil. The results showed that all kinetic models described the rate of pollutants desorption from the treated soil were succeeded to describe the rate of Zn, Cu and Ni. However, Modified Freundlich equation (MFE) was the best. All treatments significantly reduced heavy metals desorption rates, with T4 emerging as the most effective management practice. Despite, T1 enhanced Zn phytoextraction by tomatoes; However T4 reduced heavy metals accumulation in tomatoes fruits, making it a promising phytostabilization strategy for safe vegetable production. Overall, T4 represents a viable solution for alleviating heavy metals hazard in contaminated agricultural soils.