Quality assurance of the herbal formulations is the key concern of the current phytomedicinal research due to increased toxicity reports. One of the major reasons of toxicity of herbal formulations being the contamination of heavy metals in plant extracts. This guided FDA, U.S.A., to implement stringent evaluation rules for herbal formulations followed by regulations of the Indian Government for pharmaceutical industries. The aim of this research was to determine the heavy metal content of Neem (Azadirachta indica) extract and bioremediation of the polluting heavy metal ions by chelation without damaging Nimbidin, the marker compound in the present study. TLC and U.V. Spectrophotometric analysis detects the presence of Cadmium and Lead in excess to pH limits in the extract. Chelation with dithizone at different pH was the bioremediation approach for the removal of the contaminated heavy metals. The extract was analyzed in HPLC and TLC both before and after treatment with dithizone. The peak area and R value of Nimbidin when compared was found to show no significant deviations. This proves that dithizone has no interference with Nimbidin though it confiscated the toxic impurities. This method for heavy metal elimination is a potent industrial tool for Quality assurance of Herbal formulations.