The growth and metal-extraction efficiency of plants exposed to toxic metals has been reported to be enhanced by inoculating plants with certain bacteria but the mechanisms behind this process remain unclear. We report results from glasshouse experiments on Brassica juncea plants exposed to 400 mg Zn kg−1 that investigated the abilities of Pseudomonas brassicacearum and Rhizobium leguminosarum to promote growth, coupled with synchrotron based μXANES analysis to probe Zn speciation in the plant roots. P. brassicacearum exhibited the poorest plant growth promoting ability, while R. leguminosarum alone and in combination with P. brassicacearum enhanced plant growth and Zn phytoextraction. Reduced growth in un-inoculated plants was attributed to accumulation of Zn oxalate and Zn sulfate in roots. In plants inoculated with P. brassicacearum the high concentration of Zn polygalacturonic acid in the root may be responsible for the stunted growth and reduced Zn phytoextraction. The improved growth and increased metal accumulation observed in plants inoculated with R. leguminosarum and in combination with P. brassicacearum was attributed to the storage of Zn in the form of Zn phytate and Zn cysteine in the root. When combined with the observation that both bacteria do not statistically improve B. juncea growth in the absence of Zn, this work suggests that bacteria-induced metal chelation is the key mechanism of plant growth promoting bacteria in toxicity attenuation and microbial-assisted phytoremediation.