The current study aims to optimize and validate a comprehensive LC–MS/MS method for the quantification of 37 phytochemicals (15 phenolic acids, 17 flavonoids, 3 non-phenolic organic acids, 1 phenolic aldehyde and 1 benzopyrene) in Achillea species. Though Achillea species were chosen as real life samples, the current method is applicable to a wide range of plant species. The developed method was fully validated in terms of linearity, accuracy (recovery), inter-day and intra-day precision (repeatability), limits of detection and quantification (LOD/LOQ) and relative standard uncertainty (U% at 95% confidence level (k = 2)). Reversed-phase ultrahigh performance liquid chromatography was optimized to achive optimum separation for 37 phytochemical compounds and to overcome the suppression effects. MS detection was performed using a triple quadrupole mass spectrometer and negative or positive ionization modes were optimized for each analyte. Multiple reaction monitoring (MRM) was used to quantify the analytes, related molecular ions and transition ions were optimized. Phytochemical screening of ethanol and methanol-chloroform extracts of root and aerial parts of A. coarctata and A. monocephala were performed by using the developed and validated LC–MS/MS method. Root and aerial parts of both species have considerable amounts of certain phenolic-nonphenolic acids (quinic, malic, fumaric, chlorogenic and vanillic acids) and flavonoids (rutin, hesperidin, isoquercitrin, apigetrin, luteolin, apigenin). Additionally, total phenolic and flavonoid amounts, antioxidant (DPPH free radical scavenging assay, ABTS radical cation decolorization assay, β-carotene lipid peroxidation test system and CUPRAC cupper reduction capacity methods), anticholinesterase, tyrosinase, urease inhibition and cytotoxic activities (on HeLa (Human Cervical Carcinoma Cell Line) of A. coarctata and A. monocephala were also investigated. It has been determined that the studied Achillea species, that are rich in total phenolic-flavonoid and chlorogenic acid contents, have high antioxidant and cytotoxic potential at the same time. According to the results of LC–MS/MS, antioxidant and cytotoxic activity studies, after detailed chemical investigation and toxicity studies on these species, A. coarctata and A. monocephala may be promoted as promising sources of natural agents and used for the development of nutraceuticals or functional food ingredients in future.