The present study investigates S. cumini seed extracts which are considered as a promising and valuable source of bioactive compounds were prepared using different solvents such as methanol, ethanol, petroleum ether, acetone, chloroform, and diethyl ether. Among these solvents, methanol exhibited the highest extraction with a yield of 42 %. HPLC analysis revealed the highest concentration of quercetin flavonoids (49.62 mg/gm) in the methanolic S. cumini seed extract. Thus, the current work deals with the MgONPs synthesis through a biological approach using different S. cumini seed extracts. In vitro anti-oxidant properties were evaluated, which showed an IC50 value of 22.46 μg/mL for MgONPs synthesized from methanolic extract, surpassing the anti-oxidant potency of ascorbic acid by threefold. By leveraging the rich repository of bioactive compounds found within S. cumini seed extract, this study presents a novel approach to MgONPs synthesis. Exploring the symbiotic relationship between S. cumini seed extract and MgONPs, this research elucidates the pivotal role of bioactive compounds in guiding the formation and properties of nanostructures. Further anti-microbial studies on MgONPs from methanolic S. cumini seed extract were conducted against four different bacterial strains (Escherichia coli, Bacillus subtilis, Staphylococcus aureus, and S. typhimurium), revealing potent anti-microbial activity with 5.3 mm of inhibition for 100 µl against S. typhimurium. These findings suggest that S. cumini is a source of bioactive compounds responsible for the successful synthesis of MgONPs. Characterization studies of MgONPs were also carried out using UV-vis spectroscopy, FTIR, SEM, XRD, DSC and HPLC.