Eleutherine bulbosa is a plant renowned in the scientific literature for its multiple pharmacological properties. These effects are attributed to its phytochemicals, which include compounds from the naphthalene, anthraquinone, and naphthoquinone groups. The effectiveness and concentration of active biological components are greatly affected by the type of solvent selected for the extraction procedure. This study aims to compare the metabolite profiles of ethanol and water extracts from Dayak onion (E. bulbosa) and to assess their cytotoxic activities against cancer cells. Metabolite profiling was performed using an ultra-performance liquid chromatography-mass spectrometry/mass spectrometry instrument. The molecular formulas of the constituents were analyzed using MassLynx 4.1 software, while compound names and structures were identified through the PubChem database. The metabolite profiling revealed that the ethanol extract of E. bulbosa contained 32 compounds, while the water extract had 27. Analysis using a Venn diagram identified three common compounds in both extracts: 1,4-Naphthoquinone (C10H6O2), L-lysine sulfate (C6H16N2O6S), and Epirizole (C11H14N4O2). Cytotoxicity assays indicated that the ethanol extract of E. bulbosa exhibits low anticancer potential with an IC50 value of 202.37 μg/ml. In contrast, the water extract does not exhibit anticancer activity with an IC50 of 1,020 μg/ml. However, the ethanol extract has shown efficacy in initiating programmed cell death and interfering with the cell division process in T47D cancer cells. These findings suggest that an ethanol solvent is more adept at extracting the bioactive components of E. bulbosa, underscoring its potential in anticancer therapy development. Nonetheless, further research is essential to elucidate the activity of these phytochemicals and to evaluate their toxicity toward normal cells.