Environmental pollution caused by increasing levels of heavy metals (HM) is a pressing problem throughout the world. Phytoremediation is considered a prospective remediation approach for HM-contaminated soil, but more research is required to enhance remediation efficiency. Biochar is a promising bio-residue material that can be used for the sustainable remediation of heavy metal-contaminated soil. In this study, a pot experiment was conducted to investigate the effects of biochar from different bio-substrates (digestate, waste of biodiesel production from rapeseed, corn stalk) on HM (Cr, Cd, Cu, Ni, Pb, and Zn) accumulation in buckwheat and white mustard cultivated in sewage sludge-contaminated soil. The total amount of HM in soil, plant above- and below-ground biomass, leachate, and bioconcentration and translocation factors were studied to explore the mechanism of how the different bio-substrates’ biochar affects HM accumulation in selected plants. It was observed that rapeseed biochar showed the greatest significant effect in reducing the HM content in soil, plant biomass, and lysimetric water. Meanwhile, the incorporation of digestate biochar significantly increased the HM content in all the soil-plant systems and affected the HM leaching from the soil. The concentration of HM in the leachate decreased from 2.5 to 10 times. It was determined that phytostabilization is the core process of HM accumulation in buckwheat, in contrast to mustard, where the mechanism is phytoextraction. This study confirmed that biochar addition enhances the phytoremediation efficiency in soil, which can potentially improve the development of ecofriendly in-situ bioremediation technology for HM-contaminated sites.