Plant-specialized metabolites are unique sources for pharmaceuticals and industrially valuable biochemicals. Accumulation of these metabolites is common in plants stimulated by biotic or abiotic stressors and/or elicitors. One of the abiotic factors that influence the plant’s bioactive molecule is drought stress, which can be employed to stimulate the production of bioactive compounds in plants. Phyllanthus niruri is commonly used as a medicinal plant in many parts of the world for the treatment of various diseases because it contains bioactive compounds that have the potential to be antioxidants, antimicrobials, and anti-hepatoprotective. Our previous studies have demonstrated that drought stress up to 70% field capacity (FC) could increase crop production as well as phenol and flavonoid contents. This study aimed to analyze the metabolite profile of P. niruri, which was subjected to drought stress for various FC (Control, 85%, 80%, 75%, 70%, 55%). Using chromatography-mass spectrophotometry (GC-MS) analysis, forty-seven compounds were identified. Three compounds were detected in control and all treatments, whereas four compounds were only detected in drought-stressed plants. β-sitosterol, 9-tricosane, heneicosane, and hexacosane are the main compounds only detected at 80% FC. The clustering analysis revealed that drought stress induced distinct compounds compared to control. Moreover, 85% -75% FC presumably induces similar compounds as they were in the same cluster, while plants responded differently upon 70% FC and 55% FC. In conclusion, P. niruri synthesizes different bioactive compounds under different drought-stress conditions.