A novel natural low transition temperature mixture (LTTM), composed of glycerol and ammonium acetate (molar ratio 3:1), was tested for its efficacy as a solvent in recovering phenolics from chlorogenate-rich agri-food solid wastes, including potato peels (PPs), eggplant peels (EPPs), and spent filter coffee (SFC). The efficacy of this solvent was compared with other eco-friendly solvents, including aqueous glycerol, aqueous ethanol, and water. The LTTM was demonstrated to be by far the most efficient in extracting chlorogenates and superior or equally efficient with the other solvents in recovering flavonoids. LTTM extracts produced from waste were also more potent radical scavengers, but results on the reducing power were inconclusive. Liquid chromatography-diode array-mass spectrometry analysis showed that the polyphenolic profiles of all waste extracts obtained with the LTTM were rich in caffeoylquinic and p-coumaroylquinic acid conjugates.