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Herbs and agro-food wastes are rich sources of bioactive compounds vital for organisms and valuable for many fields of industry. Therefore, in this study, green deep eutectic solvents (DESs) such as choline chloride/citric acid (ChCl:CitA), glucose/citric acid (Gu:CitA), glucose/urea (Gu:U), betaine/citric acid (B:CitA), and betaine/urea (B:U) at a molar ratio of 1:1 for ultrasound-assisted extraction (UAE) of antioxidants from four herbs (chamomile—Cha, lemon balm—LB, mint—M, and nettle—N) and two agro-food wastes (buckwheat husk—BH and chokeberry pomace—ChoP) were proposed. The antioxidant capacity (AC) of the obtained extracts was evaluated utilizing three antioxidant assays: cupric reducing antioxidant capacity (CUPRAC = 0.0–429.9 μmol of Trolox (TE)/g); 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS = 0.0–146.5 μmol TE/g); and 2,2-diphenyl-1-picrylhydrazyl (DPPH = 11.9–170.3 μmol TE/g). The LB extracts revealed the highest CUPRAC (59.3–429.9 μmol TE/g), ABTS (30.7–144.3 μmol TE/g), and DPPH (32.6–170.3 μmol TE/g) values. Due to the lowest antioxidant potential of LB extracts prepared using ChCl:CitA (AC = 30.7–59.3 μmol TE/g) and the highest AC demonstrated by extracts based on B:U (AC = 144.3–429.9 μmol TE/g), the UAE conditions using a new DES consisting of ChCl and U were optimized by the Box–Behnken design (BBD). Effects of three independent variables, molar ratios of the ChCl and U (mol/mol), water content (%), and sonication time (t) on the AC of LB extracts were studied by response surface methodology (RSM). The results of principal component analysis (PCA) and hierarchical cluster analysis (HCA) demonstrated that different DESs had great differences in the extraction of antioxidant compounds from herbs and agro-food residues.