IntroductionBienertia cycloptera is a species belonging to the Chenopodiaceae family. According to earlier reports, a unique research study on the phytochemistry and biological analysis of that species was conducted.ObjectiveThis study presents an integrated metabolomics investigation combined with multivariate analysis of various extractive fractions of B. cycloptera aerial parts. This study is the first attempt to explore the anti‐inflammatory metabolites from B. cycloptera, showing its significance as a valuable traditional medicine.MethodologyBy comparing retention times, quasi‐molecular ions, and MS/MS fragment ions with databases and literature references, metabolite annotation was accomplished using ultra performance liquid chromatography (UPLC)/triple quadrupole mass spectrometry (MS). Moreover, the effects of the studied samples on the gene expression of the four pro‐inflammatory cytokines (IL‐1β, IL‐6, TNF‐α, and INF‐γ) using polymerase chain reaction (PCR) and comparing their results by those caused by piroxicam were tested to determine their anti‐inflammatory efficacy.ResultsChemical profiling revealed diverse metabolites, with 62 chromatographic peaks identified across various chemical classes. UPLC‐MS/MS of different B. cycloptera fractions unveiled distinct chemical profiles. Results showed distinct chemical compositions in each fraction, with petroleum ether fraction enriched in sterols and fatty acids; methylene chloride fraction in alkaloids, sterols, and cardenolides; ethyl acetate fraction in alkaloids, flavonoids, cardenolides, and phenolic acids; and n‐butanol fraction in flavonoids, alkaloids, and phenolic acids. Multivariate data analysis illustrated clustering patterns among petroleum ether, methylene chloride, ethyl acetate, and n‐butanol fractions. OPLS‐DA models were constructed to discern inter‐class differences, identifying discriminatory metabolites. In vitro cytotoxicity and anti‐inflammatory assays demonstrated the safety and efficacy of B. cycloptera fractions, with significant downregulation of pro‐inflammatory markers. Further analysis revealed specific metabolites associated with anti‐inflammatory effects, such as p‐hydroxybenzoic acid, vanillic acid, tachioside, ferulic acid, staphylionoside D, humilixanthin, bergaptol, vulgaxanthin I, and portulacaxanthin III.ConclusionThe findings of this study provide valuable insights into the chemical composition and bioactivity of B. cycloptera fractions, suggesting their potential as therapeutic agents and warranting further investigation.