This study aimed to understand the simple and reliable process for obtaining pelargonidin 3,5-o-diglucoside from pomegranate flowers. The process of isolating, characterizing, and exploring a constituent’s potential for natural origin is the first step in the development of new pharmacological frameworks. The investigation covers preliminary screening, titrable acidity, total phenolic, total anthocyanin, total reducing sugar content, and spectrum analysis by UV, IR, spectrofluorometric analysis, and EDS. The DPPH technique is then used to assess antioxidant activity. the 3, 5-O-diglucoside of pelargonidin. The cold maceration method removed HCl from pomegranate flowers using a green solvent methanol containing 0.1% methanolic HCl. Anthocyanins, flavonoids, and tannins are found in the methanolic pomegranate flower extract as secondary metabolites, according to preliminary screening. Total phenolic content (1.40–6.19 mg/g) of gallic acid as standard), total anthocyanin content 0.03 to 0.68 mg equivalent to cyanidin 3-glucoside (CGE)/g. UV-vis spectra showed λmax in the visible region at 502 nm. It showed strong DPPH radical activity at 85.80%, equivalent to the ascorbic acid standard. Energy dispersion X-ray analysis checked for elemental detection. The titrable acidity was found to be 1.216 in terms of citric acid. LCMS analysis for structural confirmation. Thus, the anthocyanins from agro-waste of pomegranate flowers could be the best way to extract and isolation it for commercial, pharmaceutical, and nutraceutical use.