Improvement of plant–microorganisms' interactions through microbiome engineering can enhance production of biomass and tolerance of the plants to heavy metals. The associated bacteria have profound effects on plant growth and nutrition, thus considered an important component of phytoremediation. This chapter describes the protocols on using microbes in phytoremediation of chromium-polluted soil and understanding the mechanisms of the symbiotic relationship in mitigating chromium contamination at the molecular level.