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This project aimed to apply eco-friendly extraction methods to Crocus sativus L. by-product (flowers without stigmas i.e., tepals composed of petals and sepals) to recover extracts with high antioxidant capacity and polyphenol content, to be used in cosmetic products. Flowers grown in two different Italian regions (Sample 1—Alba in Piemonte, north of Italy and Sample 2—Sibillini in Marche, centre of Italy) were subjected for the first time to different eco-friendly microwave-mediated green solvents extractions (MGSE) andquali-quantitative determination in antioxidant molecules. Firstly, the extracts from Sample 1 were selected according to their total phenol content (TPC) by Folin–Ciocalteu’s assay and antioxidant capacity (AC) by spectrophotometric assays. Then, according to preliminary results, MGSE carried out in ethanol 70°, water, and glycerin were selected as the most performing methods and applied to both Samples 1 and 2. The best results were obtained using green solvents, such as water or ethanol 70°, for the samples coming from Marche. The identification and quantification of phenolic compounds, belonging to anthocyanins and flavonols classes, was performed by using UPLC-DAD-ESI-MS. Concerning flavonols content, the most abundant analyte is kaempferol 3-O-sophoroside and the extract in water from Sample 1 showed the higher amount of flavonols, reaching the concentration of 25.35 mg of kaempferol 3-O-glucoside equivalent per gram of tepals DW of raw material. Among anthocyanins, the most abundant was delphinidin 3,5-O-diglucoside and the high concentration of anthocyanin was detected in water and ethanol extract. Two new compounds, myricetin-di-glucoside and primflasine, were identified for the first time in Crocus sativus L. by-product by high-resolution mass spectrometry (HRMS). The green batches obtained by extraction were thus characterized and evaluated for their biological potential and safety in keratinocyte HaCaT cells. The extracts were not cytotoxic up to 0.03 mg/mL. The water and ethanol 70° extracts were the most effective in counteracting oxidative stress induced by H2O2 and UVA exposure and reduced cytotoxicity induced by UVB exposure. The water extract was also able to significantly reduce cytotoxicity induced by sodium dodecyl sulphate-induced damage. Taken together, these results suggest a potential use of these waste materials as cosmeceutical preparations such as antiaging, and as anti-skin irritation formulation by-products.