Hibiscus rosa-sinesis, a well-known flowering plant in India, is used to worship Lord Ganesha. It is a member of the Malvaceae family. It is used in traditional medicine in many tropical countries to treat wounds, inflammation, fever, diabetes, infections, hair loss, and gastric ulcers. Therapeutic benefits of Hibiscus rosa-sinesis are attributed to flavonoids, tannins, terpenoids, saponins, and alkaloids. Hibiscus rosa-sinesis flowers are a good source of flavonoids, which are important components of herbal and Ayurvedic preparations. The goal of this study was to standardize the flower extract through qualitative phytochemical screening and quantitative HPTLC analysis of quercetin, an active biomarker. The result of the HPTLC analysis was compared to those obtained using HPLC. HPTLC found that the extract contained 0.33% quercetin, while HPLC found that it contained 0.37% quercetin. Further, heavy metals and trace elements were measured using atomic absorption spectroscopy (AAS). Results showed that cadmium, lead, arsenic, copper, chromium, and mercury levels (in ppm±SEM) were within acceptable limits: cadmium (0.018±0.050), lead (0.630±0.025), arsenic (0.041±0.014), copper (2.605±0.045), chromium (0.450±0.025), and mercury (0.023±0.006). This method allows standardization of plant material for raw material and finished product testing, ensuring better efficacy and safety.