To establish environmentally friendly polyphenolic extracts from grape and olive pomace, natural deep eutectic solvents (NADES) were used coupled with alternative energy sources - ultrasound and microwave irradiation. Obtained extracts were characterized by HPLC analysis, while antioxidant capacity was determined by ORAC method. Furthermore, in vitro cytotoxicity of prepared extracts was assessed by antiproliferation assay on two tumour cell lines, whereas for investigation of type of cell death or cell cycle arrest a flow cytometric analysis was applied. In addition, a detection of compounds with DNA/RNA-bindingaffinity in extracts was investigated by UV/Vis and circular dichroism spectroscopy. Grape pomace extract in NADES showed to be the best of all extracts tested, with regard to extraction of total polyphenolic compounds (p < 0.05) and related biological activities such as antioxidant and antiproliferative activity. Prepared polyphenolic extracts in NADES could be considered as ready-to-use in food and pharmaceutical industry without demanding and expensive downstream purification steps.