The phenolic composition, as well as the antioxidant and antimicrobial activities of two poorly investigated Achillea species, Achillea lingulata Waldst. and the endemic Achillea abrotanoides Vis., were studied. To obtain a more detailed phytochemical profile, four solvents with different polarities were used for the preparation of the plant extracts whose phenolic composition was analyzed using UHPLC-MS/MS (ultra-high performance liquid chromatography-tandem mass spectrometry). The results indicate that both of the investigated Achillea species are very rich in both phenolic acids and flavonoids, but that their profiles differ significantly. Chloroform extracts from both species had the highest yields and were the most chemically versatile. The majority of the examined extracts showed antimicrobial activity, while ethanolic extracts from both species were potent against all tested microorganisms. Furthermore, the antioxidant activity of the extracts was evaluated. It was found that the ethanolic extracts possessed the strongest antioxidant activities, although these extracts did not contain the highest amounts of detected phenolic compounds. In addition, several representatives of phenolic compounds were also assayed for these biological activities. Results suggest that ethanol is a sufficient solvent for the isolation of biologically active compounds from both Achillea species. Moreover, it was shown that the flavonoids naringenin and morin are mainly responsible for these antimicrobial activities, while caffeic, salicylic, chlorogenic, p-coumaric, p-hydroxybenzoic, and rosmarinic acid are responsible for the antioxidant activities of the Achillea extracts.