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Objectives: This study sought to determine the quality of essential oil from Xylopia aethiopica fruits of different geographical origins using GC‐MS‐based metabolomics, bacterial quorum sensing and anti‐inflammation assessment. Methods: Essential oil was obtained from eight batches of X. aethiopica fruits from Ghana and Nigeria by hydrodistillation, characterized using gas chromatography–mass spectrometry and differences therein found using metabolomics. The respective antibacterial activity of the oils was tested against four bacterial strains: two Gram‐positive strains, Staphylococcus aureus (ATCC 25923) and Bacillus licheniformis (ATCC12759), and two Gram‐negative strains, Escherichia coli (ATCC25922) and Klebsiella pneumoniae (ATCC 13883). Anti‐inflammation was tested using RAW 264.7 macrophage cells. Key findings: The outcome of the study revealed that the oil of the Ghana‐sourced samples exhibited superior antibacterial, cytotoxic and anti‐inflammatory effects than those from Nigeria. This could be attributed to the higher levels of the bioactive compounds present in those samples. This distinction between the samples from the two countries was clearly established using the metabolomics approach, and 14 differential metabolites were found to be potential chemical markers. Conclusions: The study lends credence to the traditional uses of the essential oil of X. aethiopica as an antimicrobial and anti‐inflammatory agent. [ABSTRACT FROM AUTHOR]