Extracts of Indonesian medicinal plants, Murraya koenigii, Syzygium polyanthum, and Zingiber purpurea were investigated for their biological activity. The presence of phytochemicals, cytotoxicity, and antimicrobial and antioxidant activities were investigated. Parts of M. koenigii, S. polyanthum, and Z. purpurea were extracted with ethanol. The extracts were evaluated for antimicrobial activity using the disc diffusion method, while antioxidant activity was determined with a 1,1-diphenyl-2-picrylhydrazyl radical scavenging assay. Cytotoxicity was investigated using the brine shrimp lethality test, and phytochemical screening was performed using a standard method. M. koenigii leaf extract exhibited the most activity in the test microorganism activity index (AI), 0.38−1.25, when compared with standard drugs. S. polyanthum ripened fruit displayed significant antioxidant activity (90%) in comparison to ascorbic acid (95%). Z. purpurea rhizome extract possessed the highest cytotoxic effect with a LC 50 of 52 μg/mL. Phytochemical analysis revealed that carbohydrate, tannin, alkaloid, steroid, triterpenoid, and flavonoid were present in the extracts of M. koenigii leaves and twigs, S. polyanthum leaves and ripened and unripe fruits, and Z. purpurea rhizome, while saponin was only present in the S. polyanthum ripened fruit extract. Our work revealed that the M. koenigii leaves, S. polyanthum ripened fruit, and Z. purpurea rhizome extracts have potential as sources of new antimicrobial, antioxidant, and cytotoxic compounds, respectively.