Over 100 species of the genus Salsola are distributed in dry, arid parts of Asia, Europe and Africa, of which many species are recognised as antifungal, anticancer, antihypertensive and anthelmintic agents. Egyptian Salsola received scant characterisation of either its phytochemical composition or its biological effects. In this study, the metabolite profiles of two Salsola species viz. S. vermiculata and S. tetrandra were characterised in the aerial portions and root via ultra-performance liquid chromatography high-resolution qTOF-MS and NMR. Identified metabolites belonged to various classes including hydroxycinnamic acid conjugates, flavonoids, oxygenated fatty acids and alkaloids. Principal component analysis of derived biochemical profiles was also used for species and/or organs classification. Roots were enriched in hydroxycinnamic acid conjugates, whereas flavonoids were more abundant in aerial parts with kaempferol derivatives as major flavonoids in S. tetrandra versus quercetin in S. vermiculata. The root of S. vermiculata exhibited strong anti-acetylcholinesterase activity relative to eserine standard.