Soap removal from crude biodiesel is considered as one of the most challenging biorefinery processes. This study reports a new technique for soap removal incorporating activated carbon (AC) in an emulsion liquid membrane (ELM) system based on deep eutectic solvents (DES-AC-ELM). These DESs were prepared from two salts, namely tetramethylammonium chloride (TMAC) and choline chloride (ChCl), with different hydrogen bond donors (HBDs) such as ethylene glycol (EG), diethylene glycol (DEG) and triethylene glycol (TEG). COSMO-RS modelling was performed in the evaluation of the activity coefficients and capacity at infinite dilution of DESs. The COSMO-RS simulation shows that the DESs with TEG as the HBD are the most effective stripping agents for soap removal which is in accordance with the experimental results. In addition, the σ-profile and σ-potential were used to investigate the interactions between the soap molecules in each phase. The impact of various process parameters on the soap removal such as the salt: HBD ratio, DES:biodiesel ratio, span-20 concentration, mixing speed, extraction time and dosage of AC were evaluated. The proposed technique achieved a soap extraction efficiency of 99.1% (6.856 ppm) and 97.5% (18.773 ppm) for TMAC:TEG(DES3) and ChCl:TEG(DES6), respectively, with a salt: HBD molar ratio of 1:4, DES:biodiesel ratio of 1:1, 2 wt% surfactant concentration, 10 min extraction duration, 400 rpm mixing speed, 0.5 treatment ratio and 0.5 wt% AC dosage. The transport mechanism of soap conforms to a first-order mass transfer behaviour, with a kinetic rate constant of 0.64 min−1 and 0.43 min−1, for DES3 and DES6, respectively. This study illustrated a new cleaner and simple route for purification of crude biodiesel.