The issue of heavy metal soil contamination is widespread, and the negative effects of heavy metals on the ecosystem depend on their chemical speciation in contaminated soil. Pomelo peel-derived biochar produced at 300 °C (PPB300) and 500 °C (PPB500) and its combination with apatite ore (AP) was applied to immobilize lead (Pb) and zinc (Zn) in agricultural multi-metal polluted soil. Soil amendments including biochar (PPB300 and PPB500) at concentrations of 3%, 5%, and 10%, as well as a mixture of biochar and apatite (AP) at 3:3% and 5:5% weight ratios, were introduced into the soil matrix. The chemical forms of Pb and Zn in incubated soil samples and control soil (CS) were studied utilizing the Tessier’s sequential extraction procedure. The chemical partitioning of heavy metals was carried out using Tessier’s extraction protocol, yielding fractions representing exchangeable (F1), carbonate (F2), Fe/Mn oxide (F3), organic matter (F4), and residual (F5) forms. Quantification of Pb and Zn concentrations was accomplished via inductively coupled plasma mass spectrometry (ICP-MS). Observations revealed notable elevations in pH, organic carbon (OC), and electrical conductivity (EC) levels within the treated soil relative to the control soil (p < 0.05). After incubating PPB300, PPB500, and AP for 30 days, there was a reduction in the exchangeable fraction of Pb and Zn by approximately 64% and 58% respectively. This reduction was achieved by transforming heavy metals from mobile fractions to immobile fractions using five primary mechanisms: chemical and physical adsorption, electrostatic attraction, the formation of complexes via interactions with active groups, cation exchange processes, and precipitation events mediated by phosphate, carbonate ions, or hydroxyl ions within an alkaline environment. Therefore, pomelo peel-derived biochar and the blend of biochar/apatite show promise as materials for mitigating heavy metal pollution in soil.