The therapeutic importance of Allium cepa L. has been well established through ethnobotanical studies. Malachite Green is a highly toxic dye that finds extensive use in the textile industry as a fabric colorant. A. cepa was treated with malachite green solutions (20mg/l and 40mg/l) for 45 days. The roots actively take up malachite green and impede the plant's growth in root length, shoot length and fresh weight. A. cepa is rich in bioactive compounds, which have superior antioxidant and antimicrobial properties. We observe that the antimicrobial activities decrease by 36% for Staphylococcus aureus and 31% for Escherichia coli on the treatment of A. cepa bulbs with 40 mg/l malachite green. Antioxidant activity was similarly lowered by 61% under the toxic effects of the dye. Reduction in the efficacy of A. cepa in terms of the critical medicinal properties and general retardation in growth is a cause of concern. This article reports a previously unknown aspect of malachite green toxicity and presents the effect of any dye on the medicinal properties of A. cepa for the first time.