The mechanisms of soil Cd and Pb alterations and distribution following biochar (BC; 0 to 40 t ha−1) amendments applied (in either 2009 [long-term] or in 2016 [short-term]) to a contaminated rice paddy soil, and subsequent plant Cd and Pb tissue distribution over time was investigated. Water-soluble Cd and Pb concentrations decreased by 6.7–76.0% (short-term) and 10.3–88.1% (long-term) with biochar application compared to the control. The soil exchangeable metal fractions (i.e., considered more available) decreased, and the residual metal fractions (i.e., considered less available) increased with short- and long-term biochar amendments, the latter likely a function of biochar increasing pH and forcing Cd and Pb to form crystal mineral lattice associations. Biochar application reduced Cd (16.1–84.1%) and Pb (4.1–40.0%) transfer from root to rice grain, with rice Cd and Pb concentrations lowered to nearly Chinese national food safety standards. Concomitantly, soil organic matter (SOM), pH and soil water content increased by 3.9–49.3%, 0.05–0.35 pH units, and 3.8–77.4%, respectively, with increasing biochar application rate. Following biochar applications, soil microbial diversity (Shannon index) also increased (0.8–46.2%) and soil enzymatic activities were enhanced. Biochar appears to play a pivotal role in forcing Cd and Pb sequestration in contaminated paddy soils, reducing heavy metal transfer to rice grain, and potentially leading to reduced heavy metal consumption by humans.