The industrial implementation of new eco-friendly solvents has highlighted the need to analyse both the structures and thermophysical properties of these solvents. Here, two deep eutectic solvents (DESs) used in the agro-food field were studied: xylitol:choline chloride:water (1:2:3 M ratio), XoCH, and citric acid:choline chloride:water (1:1:6 M ratio), CiCH. The H-bond network between the components of each DES was evaluated and the diffusion coefficients at 298.15 K were calculated using NMR spectroscopy. In addition, seven thermophysical properties were determined from 278.15 to 338.15 K. Also, the solubility of quercetin in water and in the two eutectic mixtures was measured and the interactions between components were studied. NMR experiments revealed the presence of water within the supramolecular structure of XoCH, but CiCH is a “DES-in-water” solution. Based on the results, XoCH is the most compact mixture. Finally, quercetin was remarkably more soluble in the studied DESs than in pure water.