In order to improve the accuracy and consistency of control phytomedicine preparations worldwide, regulatory authorities are requesting research into new analytical methods for the stricter standardisation of phytomedicines. Such methods have to be both objective and robust, and should address the reproducibility of the content of the chemical profiles. NMR-based metabolomics, which combines high-resolution H-1-NMR spectroscopy with chemometric analysis, has been employed as an innovative way to meet those demands. In this paper, chamomile flowers from three different geographical regions, namely, Egypt, Hungary and Slovakia were characterised using H-1-NMR spectroscopy followed by principal component analysis. it was found that the origin, purity and preparation methods contributed to the differences observed in prepared chamomile extracts. In addition, this method also enabled the elucidation of the molecular information embedded in the spectra responsible for the observed variability. The metabolomic strategy employed in the current study should provide an efficient tool for the quality control and authentication of phytomedicines.