This study investigated the use of deep eutectic solvents (DESs) for separating azeotropic mixtures of alcohol-ester systems. The DESs were composed of choline chloride combined with either malonic or glutaric acid. Liquid-liquid equilibria (LLE) data and phase diagrams were obtained for pseudoternary systems including ethanol-n-propyl formate, n-propanol-n-propyl formate, and n-butanol-n-propyl formate at temperatures of 293.15 and 313.15 K and 101.3 kPa. Liquid-liquid tie lines were determined and analyzed by using 1H NMR spectroscopy. The separation performance of DESs was characterized by distribution coefficients and selectivity values. The studied DESs demonstrated the ability to catalyze transesterification reactions. Conversion values in the organic phase were determined as a function of alcohol concentration. This research provides valuable insight into the potential use of choline-chloride-based DESs for separating azeotropic mixtures, particularly in alcohol-ester systems while also revealing their catalytic properties in transesterification reactions.