Deep eutectic solvents (DES) are attracting a lot of attention as a green alternative to hazardous organic solvents for the extraction of valuable bioactive compounds from agricultural and processing wastes. In this study, the simultaneous extraction and deglycosylation of quercetin derivatives from apple pomace was achieved through the use of various DES from choline chloride and various carboxylic acids. The content of quercetin derivatives was similar in DES and conventional methanol extracts, but their relative amounts were significantly different due to deglycosylation during DES extraction. Chromatographic and spectroscopic analyzes made it possible to determine the structures of the glycosylated quercetins and showed that the proportion of quercetin aglycon in DES extracts can be controlled by the DES composition, extraction temperature and extraction time. Of all the quercetin glycoconjugates present, quercetin 3-O-α-arabinofuranoside was more prone to deglycosylation during DES extraction than any other quercetin derivative. In addition, the antioxidant activity of the DES extracts was higher than that of the methanol extracts, probably due to the increase in quercetin aglycone content during the extraction. These data show the potential to extract and deglycosylate quercetin derivatives in a single step with green DES to create bioactive compounds with increased activity.