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The potential applications of Achillea species in various industries have encouraged the examination of their phytochemical components along with their biological potential. In the present study, phenolic contents and essential oil compositions together with the in vitro biological activities of the aerial parts from Achillea biebersteinii Afan. and Achillea millefolium subsp. millefolium Afan. collected from Turkey were evaluated. Different solvent extracts (n-hexane, chloroform, methanol, water) were prepared and their antimicrobial, anticholinesterase, and antioxidant activities were studied. The LC-MS/MS results revealed the presence of 16 different phenolic compounds, including chlorogenic acid, rutin, quercetin, and luteolin glycosides, in methanolic extracts. According to GC-FID and GC/MS results, the primary components of the oils were identified as 1,8-cineole (32.5%), piperitone (14.4%), and camphor (13.7%) in A. biebersteinii and 1,8-cineole (12.3%) and β-eudesmol (8.9%) in A. millefolium subsp. millefolium. The infusion and methanolic extracts of both species were found to be rich in their total phenolic content as well as their antioxidant and anticholinesterase activity. In contrast, the n-hexane and chloroform extracts of both species showed strong antimicrobial activity with MIC values ranging from 15 to 2000 μg/mL. Our findings suggest that the investigated Achillea species could be evaluated as potent natural agents, and further studies into the promising extracts are needed.