In what is believed to be the first study of its kind, the compositions of the toxic and allelopathic weed parthenium, and its vermicompost, have been investigated using UV-visible and Fourier transform infrared spectroscopy, thermogravimetric analysis, differential scanning calorimetry, gas chromatography-mass spectroscopy, and scanning electron microscopy. The studies reveal that the weed is transformed into a totally benign organic fertilizer during the course of its vermicomposting. This is indicated by substantial improvements in the humification index, mineralization of organic matter, and degradation of complex aromatics such as lignin and polyphenols into simpler carbohydrates and lipids when parthenium is turned into its vermicompost. There are also significant fragmentation, bio-oxidation and molecular rearrangements of chemical compounds in parthenium vermicompost compared to the parent substrate. In particular, parthenin, which is principally responsible for the toxicity and allelopathy of parthenium, is completely degraded by the vermicomposting of parthenium. The study opens the way to profitable use of the millions of tonnes of parthenium that are generated annually, the continued proliferation of which causes great loss of biodiversity.