Soil contamination is increasingly a global problem with serious implications for human health. Among different soil decontamination approaches, electrokinetic (EK) remediation is a relatively new technology for treating organic and inorganic contaminants in soil. This research aims to develop an enhanced EK treatment method incorporating a compost-based reactive filter media (RFM) with the advantages of low-cost and strong affinity for heavy metals and test and improve the treatment efficiency for multiple heavy metals in natural soil. A series of EK operations were performed to investigate the performance of EK-RFM under different operating conditions such as the electric current and voltage, processing time, and the amount of RFM. The electric current and treatment time demonstrated a significant positive impact on removing Zn, Cd and Mn ions while changing the amount of RFM had an insignificant impact on the efficiency of heavy metals removal. Overall, 51.6%–72.1% removal of Zn, Cd, and Mn was achieved at 30.00 mA of electric current and 14 days of treatment duration. The energy consumption of the EK process was 0.17 kWh kg−1. The soil organic matter adversely affected the mobilization and migration of heavy metals such as Cu and Pb during EK treatment. The results are valuable in optimizing the design of the EK-RFM system, which will extend its application to field-scale soil decontamination practices.