This study is a comprehensive account of microscopic assessment of flower of Achillea santolina L., a medicinally important species of the genus Achillea from Pakistan. The study was aimed to provide data for the quality control and standardization of A. santolina L. flower. The microscopic characterization has been carried out through light microscopy and scanning electron microscopy. Various characteristic histological features of phyllaries, ray floret, disc floret, anther wall, filament, stigma, style, and ovary were observed. The pollens were found as tricolporate, spheroidal while the surface ornamentation was echinate. Qualitative and quantitative palyno‐anatomical assessment was carried out through scanning electron microscopy. The exine thickness and the width of spines were calculated. The P/E ratio characterized the shape of pollen as oblate‐spheroidal and sub‐oblate in polar and equatorial views respectively. The elemental analysis of the flower through SEM–EDX showed the presence of various elements. Phytochemical screening of flower showed the presence of carbohydrates, flavonoids, fixed oils, glycosides, phenols, steroids, tannins, terpenoids, and coumarins. UV–vis spectra of the ethanol extract showed characteristics peaks in both ultraviolet and visible regions. This work will provide a standard reference for the correct identification of A. santolina L. an important aspect in the quality control. Additionally, the data produced by phytochemical, elemental and florescence analysis, and UV–visible spectroscopy will help in developing standards for this herb that will be useful for research and development and manufacturing of herbal products.