Background Deep eutectic solvents (DES) have emerged as effective solvents that address many challenges in analytical chemistry, particularly in microextraction. However, until now, their use has been primarily focused on extraction processes. This has significantly limited their application in analytical chemistry, especially in flow analysis, where the high viscosity of DES has made their use difficult. Results This paper presents a novel DES-based liquid-liquid microextraction approach for the separation and determination of trace metals in foods using an automated flow analysis system. In this study, a DES composed of thymol and thionalide was first prepared and thoroughly characterized by spectroscopic (IR, NMR) and differential scanning calorimetry techniques. The COSMO-SAC model was employed to predict the solubility of metal salts (Cu, Cd, Pb, and Hg) in the new DES. The solvent was applied to glass fiber as a stationary phase in an extraction column in a flow analysis. After microwave digestion of food samples, metals were extracted by this DES in an automated mode and subsequently eluted with an aqueous thiourea solution. The procedure demonstrated limits of detection (LOD) of 6 μg kg−1 for mercury, 4 μg kg−1 for copper, 6 μg kg−1 for lead and 0.6 μg kg−1 for cadmium. Significance This study represents the first application of a DES-based stationary phase in automated flow analysis, significantly enhancing extraction efficiency. The procedure enables precise and reliable determination of trace metals in food products, aligning with green chemistry principles by minimizing waste.