Herbal medicine-based therapies are an essential trait for cancer treatment due to their competency and less side effects. Indigofera aspalathoides Vahl ex DC., Fabaceae, is a well-known traditional medicinal herb that is habituated mainly in South India and Sri Lanka. The previous reports state that the crude plant extract possesses anti-inflammatory, anti-tumor, and anti-oxidant properties, however the effects of bioactive molecules from the plant have not yet been studied. Here, we have investigated the anticancer property of lead biomolecule from I. aspalathoides targeting matrix metalloproteinases (MMP-2 and MMP-9), which inhibits cancer metastasis and promotes cell death in breast cancer (MDA-MB-231) and prostate cancer (PC3) cell lines. A semi-purified lead biomolecule indigocarpan was obtained from ethyl acetate extract using chromatographic techniques. The major active molecule indigocarpan was tested for its cytotoxicity and the IC50 values were found to be 92 mu g/ml (MDA-MB-231) and 93 mu g/ml (PC3) and 135 mu g/ml (A549), respectively, and further, the effect of drug molecule was assessed to study the morphological changes in both cell lines (MDA-MB-231 and PC3) and no such alterations were observed when indigocarpan was treated with L-132 normal cell line. It also demonstrated that indigocarpan exhibits robust anti-metastatic activity as it significantly inhibited cell-cell contact, cell migration, matrix metalloproteinases (MMP2 and MMP9) expression, and activity in both cell lines. Acridine orange/ethidium bromide staining differentiated the live cells, and the drug-induced early and late apoptotic cells in both cancer cells. The intracellular ROS accumulation was evaluated by using a DCFH-DA assay fluorescent probe to determine the apoptotic effects of the indigocarpan. Hence, from our study, partially purified indigocarpan from I. aspalathoides acts as a potent drug that controls cancer metastasis and induces cell death to prevent breast and prostate cancer.