Eryngium is the largest and most complex genus in family Apiaceae, widely employed in folk medicine as hypoglycemic, antitussive, kidney stone inhibitor, diuretic, aphrodisiac, and anti-inflammatory due to having a considerable number of secondary metabolites and biologically active chemical compounds such as polyacetylenes, coumarins, flavonoids, phenolics, terpenoids, triterpenoid saponins and steroids. In this study, the effects of extracting solvent, organ selection as well as the habitat of E. campestre ecotypes growing in Egypt were evaluated on its chemical profile and antimicrobial activity against six pathogens using Near-Infrared spectroscopy and HPTLC-image analysis, each combined with multivariate analysis. The results showed that different organs of the tested species showed variant metabolomic profiles, together with the geographical origin, being a less profoundly influential factor on the chemical profile, and subsequently the biological activity of the tested samples. supervised and unsupervised pattern recognition on data of NIR and HPTLC techniques, it was possible to differentiate four clusters: two different habitats, two plant parts (Shoot and Root) as well as the five solvent fractions of each plant sample.