Increased depletion of existing fossil fuel reserves and the associated deterioration of the environment have led to the need for the development of alternative, environmentally acceptable and economically feasible energy sources. Biofuels produced from sustainable feedstocks, such as vegetable oils and animal fats, represent a promising solution to these problems. Due to its beneficial properties, biodiesel stands out as a clean and efficient substitute for petroleum-based diesel. However, before its use as a final product, it is necessary to achieve a satisfactory quality of biodiesel. Therefore, the process of biodiesel purification, during which the present by-products and impurities are removed, is essential. In this paper, continuous biodiesel purification was carried out. Biodiesel was obtained by transesterification using methanol and with the alkaline catalyst KOH at 60 °C. Waste cooking oil provided by the licensed collector Agroproteinka d.o.o. was used as feedstock. For purification, continuous extraction was carried out at room temperature using deep eutectic solvent choline-chloride/ethylene-glycol in a molar ratio of 1:2,5. The extraction took place in a reciprocating plate column (Karr column). Plates of the same geometry made of two different materials, steel and polyethylene terephthalate glycol (PETG), were used. The influence of plate material on the extraction efficiency of glycerol and glycerides from crude biodiesel was examined. The extraction efficiency was also influenced by the solvent to biodiesel ratio and the pulsation frequency of the plates. Qualitative analysis of raw material, crude and refined biodiesel included FTIR and NMR spectroscopy, and gas chromatography was applied for quantitative analysis.