Lead is one of the most toxic elements on earth. The harmful effects of lead at higher concentrations were seen on plant vegetation because plants are directly exposed to toxic levels. A previous work with B. juncea varieties were already screened against Pb to assess their endurance capacity from which B. juncea P. Vijay was opted out as the most tolerant, and B. juncea PM 25 was selected as the sensitive cultivar. Indian mustard, a well-known hyperaccumulator plant, is the most promising environmental crop used in diverse situations for ecological clean-up, and a chelating agent, EDTA, having remarkable efficacy, was used in the experiment. In the present study, the pot experiment was conducted in soil pretreated with 1000 mgkg− 1 Pb soil, and pots were augmented with different EDTA (2–10 mmol) concentrations. All the growth parameters were reduced more drastically in plants treated with Pb, however, a non-significant reduction was observed in 5 mmol EDTA treatments. Photosynthetic pigments, yield, nitrate reductase activity, NPK content were affected negatively, in contrast superoxide dismutase, catalase activity, and the ratio of chl a and chlb were increased in Pb and Pb + EDTA treated both varieties. All the parameters of PM 25 variety were affected more than P. Vijay during the experiment. Pb accumulation was elevated significantly by the augmentation of up to 5mmol EDTA in both cultivars. Accumulation of Pb in the shoot was higher in PM 25 than in P. Vijay, whereas root Pb accumulation shows the opposite, i.e., more Pb in roots of P. Vijay than PM 25. However, P. Vijay was found to be more effective in terms of Pb accumulation per plant than PM 25. Hence in the present work, we found that augmentation of Pb-polluted soil with EDTA works well while dealing with B. juncea assisted phytoremediation, and P. Vijay were found to be stronger candidate than PM 25. Also, we found that 5 mmol of EDTA was optimum for phytoremediation of the soil polluted with up to 1000 mg Pb kg− 1 soil.