This study focuses on the phytochemical analysis of the aerial parts of three Alkanna species: A. orientalis (L.) Boiss., A. tinctoria Tausch. and A. kotschyana A. DC. (Boraginaceae) growing wild in the Mediterranean basin, as mostly the roots of the genus have been widely researched. Their methanol extracts were subjected to qualitative LC-MS analyses, resulting in the annotation of 28 different secondary metabolites, with 27 originating from A. orientalis, 25 from A. tinctoria and 23 from A. kotschyana. The detected metabolites are categorized into three chemical types: organic acids (2), flavonoids and their glycosides (17), and caffeic acid derivatives (9). Furthermore, the chemical profiles of the three species are discussed chemotaxonomically. Caffeic acid and its derivatives, along with glucosides of quercetin and kaempferol, were identified in all three studied species. Additionally, their total phenolic and flavonoid contents were determined. The antioxidant capacity was evaluated through various chemical assays, as well as their in vitro enzyme inhibitory properties towards cholinesterases (AChE and BChE), α-amylase and α-glucosidase. The results showed that A. tinctoria exhibited the strongest antioxidant activity (211 mgTE/g extract in DPPH and 366 mgTE/g extract in ABTS), probably due to its high total phenolic (53.3 mgGAE/g extract) and flavonoid (20.8 mgRE/g extract) content, followed by A. kotschyana. These chemical and biological findings provide valuable insights for potential promising applications of the aerial parts of the species outside of the well-known uses of their roots.