Echinacea purpurea (L.) Monech has a diverse range of phytochemicals, including flavonoids, polyphenols, phenolic acids, alkylamides, and terpenoids. Phenolic and flavonoid substances derived from the leaves and flowers have been used for treatment of illness. The aim of this study to evaluate the polyphenolic components of the flowers and leaves of E. purpurea, along with the diurnal variations and the morphological differences. Two-year-old in full bloom flowers and leaves were harvested at different times of the day (6:00 am, 9:00 am, 12:00 am, 03:00 pm, 06:00 pm, 09:00 pm). The water and methanol extracts prepared from these samples to determine total phenolic, total flavonoid and phenolic compound contents. The experiment was established in randomized complete block design with three factors and three replications. The highest total phenolic content was observed in flowers with methanol extract (157.91 ± 0.32 mg QE/g dry extract) at 09.00 a.m. Also the highest total flavonoid content was observed in leaves with methanol extract at 09.00 a.m (80.12 ± 0.16 mg QE/g dry extract). Chlorogenic acid (19.1 ± 0.83 mg/g methanol extract) and caffeic acid (13.2 ± 0.58 mg/g methanol extract) were identified as the predominant phenolic acids. The peak concentrations of these phenolic acids were observed at 6:00 a.m, followed by a gradual decline throughout the subsequent hours of the day. Findings emphasize the importance of harvesting E. purpurea at the optimal time to maximize antioxidant capacity. This study provides valuable new information on morphogenetic and diurnal variation of phenolic and flavonoid content for drug and pharmaceutical raw material production.