Medicinal plants have been a major source of biologically active natural products and are used as medicines to cure disases in all cultures since ancient times. Cassia angustifolia (senna) and Trigonella foenum-graceum (fenugreek), are medicinal herbs, recommended by Prophet Muhammad (Peace be upon him), used in Muslim ethnobotanical culture. These herbs have traditionally been used against liver diseases, constipation, typhoid, cholera, cancer, diabetes, high cholesterol, ulcer, and inflammations etc. The present study describes isolation and identification of biologically active compounds, selected based on their bioactivity, from C. angustifolia and T. foenum-graceum. The pharmacological activities; antibacterial, antioxidant, anticancer, neuroprotective and hepatoprotective effects of C. angustifolia and T. foenum-graceum were investigated from their aqueous and organic (methanol, ethanol, acetone and ethyl acetate) extracts. Phytochemical screening revealed the presence of steroids, alkaloids, terpenoids, flavonoids, coumarins, cardiac glycosides, saponins, anthraquinones, phenols and tannins in both plant extracts. Methanol and ethyl acetate extracts of both plants possess antibacterial, antioxidant, anticancer, neuroprotective and hepatoprotective activities which led to the isolation and identification of active compounds. A novel compound (proposed name “Irizoflavan”) and three known flavonoids i.e. Quercimeritrin, Scutellarein, and Rutin were isolated from C. angustifolia. Two known flavonoids i.e. Amurensin and Cosmosiin were isolated from T. foenum-graecum. These compounds were isolated and reported for the first time from these plants. The present work provides basis for the in depth understanding of the molecular pathways associated with these isolated compounds and for the development of plant based drugs.