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Moringa oleifera, a nutrient-rich medicinal plant, has garnered growing scientific interest due to its diverse pharmacological properties. In this study, spectroscopic analysis, coupled with cytotoxic, antiviral, and antioxidant properties testing, was followed by gene expression analysis of various fractionated Moringa oleifera extracts to assess their potential biomedical applications. Ethanolic leaf extract was fractionated using solvents with increasing polarity (hexane, methylene chloride, ethyl acetate, and butanol). Cytotoxicity was tested against multiple cancer cell lines and normal cells, while antiviral activity was assessed against HAV ( Hepatitis A virus) and HSV-1/2 (Herpes simplex virus type 1/type 2). Antioxidant capacity was evaluated using DPPH assays. Gene expression of BAX and BCL-2 was analyzed by qRT-PCR to understand apoptotic pathways. Chemical profiling was performed using LC–MS/MS and GC–MS. The hexane fraction showed potent cytotoxicity against cancer cell lines MCF-7 (breast carcinoma) and HepG-2 (hepatocellular carcinoma), with low toxicity to normal PBMCs (normal human primary peripheral blood mononuclear cells). The butanol fraction displayed strong antiviral activity, particularly against HAV and HSV strains, while the ethyl acetate fraction exhibited the strongest antioxidant activity. The pro-apoptotic BAX gene was upregulated while the anti-apoptotic BCL-2 gene was downregulated, according to gene expression analysis. Metabolomic profiling identified over 60 bioactive compounds, including phenolic acids, flavonoids, and terpenoids, which were consistent with the observed biological activities. These findings characterize Moringa oleifera as a rich source of multifunctional bioactive compounds and provide a preliminary in vitro foundation for its potential application in selective anticancer and antiviral therapies.