There have been no reports published on the rare Echinops taeckholmiana growing wildly in Egypt. So, this study aimed to preserve it through method optimization of in vitro seed germination, besides callus formation from induced seedlings. Chemical profiling using gas chromatography-mass spectrometry (GC-MS) analysis of the n-hexane fraction afforded 29 identified components, mainly fatty acids esters, sesquiterpenes, triterpenes, one thiophene, and bis(2-ethylhexyl) phthalate. Ultra-performance liquid chromatography-electron spray ionization/tandem mass spectrometry (UPLC-ESI/MS-MS) analysis of total alcoholic root and induced calli extracts resulted in 68 metabolites. Taraxeryl acetate, β-sitosterol, stigmasterol-3β-D-glucoside, and 1,1,1-kestopentaose were identified from the defatted root extract, which inhibited α-amylase (IC50 54.6 μg/mL) and α-glucosidase (60.4 μg/mL) enzymes compared with acarbose (IC50 values of 30.57 and 34.71 μg/mL, respectively). Moreover, it showed moderate activity against HepG2 (IC50 31.1 ± 1.4 μg/mL) and no activity against M-NFS-60 cell lines compared to cisplatin (IC50 3.25 ± 1.4 and 8.37 ± 0.25, respectively).