This study investigates the underutilized potential of agri-crops from the Asteraceae family by employing sustainable and green technologies (supercritical fluid, ultrasound, and Soxhlet extractions) to enhance the recovery of bioactive compounds. A total of 21 extracts from native and waste seeds of dandelion, milk thistle, and chamomile were systematically compared utilizing a combination of solvents (supercritical CO2 and absolute or aqueous ethanol). Supercritical CO2 extraction yielded up to 281 mg/g of oils from native seeds, while conventional techniques with ethanol recovered an additional 142 mg/g of extracts from waste seeds. Notably, waste seed extracts exhibited superior biological activity, including potent antioxidant properties (IC50 values as low as 0.3 mg/mL in the DPPH assay) and broad-spectrum antimicrobial activity against 32 microbial strains, including methicillin-resistant Staphylococcus aureus, Gram-negative bacteria, and yeast strains. Phenolic compounds were abundant, with up to 2126 mg GAE/g, alongside 25.9 mg QE/g flavonoids, and 805.5 mg/kg chlorophyll A. A selective anticancer activity of waste milk thistle extracts was observed, with a selectivity index of 1.9 to 2.7. The oils recovered from native seeds demonstrated lower bioactivity and are well-suited for applications in food. The potent bioactivity of the smaller quantities of waste seed extracts positions them as valuable candidates for pharmaceutical use. Keywords: supercritical carbon dioxide extraction; edible oils isolation; antimicrobial activity; antioxidant activity; cytotoxicity; biological activity; phytochemical isolation; natural food resources