Achillea millefolium L. herb and flowers have high biological activity; hence, they are used in medicine and cosmetics. The aim of this study was to perform morpho-anatomical analyses of the raw material, including secretory tissues, histochemical assays of the location of lipophilic compounds, and quantitative and qualitative analysis of essential oil (EO). Light and scanning electron microscopy techniques were used to analyse plant structures. The qualitative analyses of EO were carried out using gas chromatography-mass spectrometry (GC/MS). The results of this study showed the presence of exogenous secretory structures in the raw material, i.e., conical cells (papillae) on the adaxial surface of petal teeth and biseriate glandular trichomes on the surface flowers, bracts, stems, and leaves. Canal-shaped endogenous secretory tissue was observed in the stems and leaves. The histochemical assays revealed the presence of total, acidic, and neutral lipids as well as EO in the glandular trichome cells. Additionally, papillae located at the petal teeth contained neutral lipids. Sesquiterpenes were detected in the glandular trichomes and petal epidermis cells. The secretory canals in the stems were found to contain total and neutral lipids. The phytochemical assays demonstrated that the A. millefolium subsp. millefolium flowers contained over 2.5-fold higher amounts of EO (6.1 mL/kg) than the herb (2.4 mL/kg). The EO extracted from the flowers and herb had a similar dominant compounds: β-pinene, bornyl acetate, (E)-nerolidol, 1,8-cineole, borneol, sabinene, camphor, and α-pinene. Both EO samples had greater amounts of monoterpenes than sesquiterpenes. Higher amounts of oxygenated monoterpenes and oxygenated sesquiterpenoids were detected in the EO from the herb than from the flowers.