Globally, open-pit coal mining is associated with severe land use impact and the contamination of soil and water resources with heavy metals. Thus, in growing economies like India, where coal is a significant energy source, the heavy metals contamination of soil and water become ubiquitous. This study uses a unique remediation approach by developing biochar-bentonite-based seed balls encapsulating Shorgham grass seeds at their core for application in the contaminated soil. The seed ball was developed by using the bentonite biochar composite in varying weight fractions of 0.5–5% with respect to the kaolinite, whose fractions in the seed ball also varied at one, three, and five parts. The seed balls were applied to the pots containing 3 kg of heavy-metals-contaminated soil for a pot-culture study in a polyhouse for a period of four months. Initial soil analysis results indicated that the mine soil samples showed poor nutrient and organic matter content and were contaminated with heavy metals such as Ni, Zn, Cr, and Cd. Post-pot-culture soil analysis results indicated that the application of seed balls containing five fractions of biochar composite with its combination with three and five-weight fractions of kaolinite showed substantial improvement in the pH, available nutrients, organic matter content, soil enzymes, and overall soil fertility index compared to the controlled study and other cases. The same combination of seed balls also significantly reduced the plant-available fractions of Ni, Zn, Cr, and Cd in the soil, indicating the stabilization of heavy metals within the soil matrix. Also, the application of seed balls substantially improved the plant physiology and reduced the release of stress hormones within the plant cells, indicating improvement in the plant’s biotic and abiotic stress factors. Thus, the application of seed balls in heavy metals contaminated soils, particularly over a large stretch of land, could be a low-cost and viable remediation technique.